片段文件:How to use mega software.mp4的中文（中国大陆）‎字幕

Kind: captions Language: en 00:00:00,170 --> 00:00:02,990 align:start position:0% all welcome</c> 00:00:02,990 --> 00:00:03,000 align:start position:0% all right good morning everybody welcome 00:00:03,000 --> 00:00:04,640 align:start position:0% all right good morning everybody welcome thank Maker</c> 00:00:04,640 --> 00:00:04,650 align:start position:0% thank you for coming to the Maker 00:00:04,650 --> 00:00:07,210 align:start position:0% thank you for coming to the Maker workshop Glenn</c> 00:00:07,210 --> 00:00:07,220 align:start position:0% workshop so you all know me I'm Glenn 00:00:07,220 --> 00:00:09,350 align:start position:0% workshop so you all know me I'm Glenn and use</c> 00:00:09,350 --> 00:00:09,360 align:start position:0% and I'm going to talk about how to use 00:00:09,360 --> 00:00:11,870 align:start position:0% and I'm going to talk about how to use mega we're</c> 00:00:11,870 --> 00:00:11,880 align:start position:0% mega CC and analysis pipelines we're 00:00:11,880 --> 00:00:15,049 align:start position:0% mega CC and analysis pipelines we're analyzing so</c> 00:00:15,049 --> 00:00:15,059 align:start position:0% analyzing molecular sequence data so 00:00:15,059 --> 00:00:19,130 align:start position:0% analyzing molecular sequence data so first a</c> 00:00:19,130 --> 00:00:19,140 align:start position:0% first of all what is mega xcc Omega is a 00:00:19,140 --> 00:00:22,400 align:start position:0% first of all what is mega xcc Omega is a software comparative</c> 00:00:22,400 --> 00:00:22,410 align:start position:0% software or physics based comparative 00:00:22,410 --> 00:00:24,080 align:start position:0% software or physics based comparative analysis data</c> 00:00:24,080 --> 00:00:24,090 align:start position:0% analysis but like a merge sequence data 00:00:24,090 --> 00:00:26,800 align:start position:0% analysis but like a merge sequence data based and</c> 00:00:26,800 --> 00:00:26,810 align:start position:0% based on evolutionary principles and 00:00:26,810 --> 00:00:29,300 align:start position:0% based on evolutionary principles and mega molecular</c> 00:00:29,300 --> 00:00:29,310 align:start position:0% mega is an acronym for molecular 00:00:29,310 --> 00:00:32,900 align:start position:0% mega is an acronym for molecular evolutionary in</c> 00:00:32,900 --> 00:00:32,910 align:start position:0% evolutionary genetics analysis the X in 00:00:32,910 --> 00:00:35,000 align:start position:0% evolutionary genetics analysis the X in the version</c> 00:00:35,000 --> 00:00:35,010 align:start position:0% the name signifies that this is version 00:00:35,010 --> 00:00:36,459 align:start position:0% the name signifies that this is version 10 multi-platform</c> 00:00:36,459 --> 00:00:36,469 align:start position:0% 10 and also that it's a multi-platform 00:00:36,469 --> 00:00:38,840 align:start position:0% 10 and also that it's a multi-platform application running</c> 00:00:38,840 --> 00:00:38,850 align:start position:0% application it's currently running 00:00:38,850 --> 00:00:40,580 align:start position:0% application it's currently running natively soon</c> 00:00:40,580 --> 00:00:40,590 align:start position:0% natively on Windows and Linux in soon 00:00:40,590 --> 00:00:43,970 align:start position:0% natively on Windows and Linux in soon we'll C</c> 00:00:43,970 --> 00:00:43,980 align:start position:0% we'll have a Mac OS version out C C 00:00:43,980 --> 00:00:46,430 align:start position:0% we'll have a Mac OS version out C C stands the</c> 00:00:46,430 --> 00:00:46,440 align:start position:0% stands for computing core so this is the 00:00:46,440 --> 00:00:51,049 align:start position:0% stands for computing core so this is the calculation maybe</c> 00:00:51,049 --> 00:00:51,059 align:start position:0% calculation engine Omega and Megas maybe 00:00:51,059 --> 00:00:52,279 align:start position:0% calculation engine Omega and Megas maybe next of</c> 00:00:52,279 --> 00:00:52,289 align:start position:0% next C C is different than a lot of 00:00:52,289 --> 00:00:53,959 align:start position:0% next C C is different than a lot of command did</c> 00:00:53,959 --> 00:00:53,969 align:start position:0% command line applications so we did 00:00:53,969 --> 00:00:55,250 align:start position:0% command line applications so we did actually two</c> 00:00:55,250 --> 00:00:55,260 align:start position:0% actually distribute this with two 00:00:55,260 --> 00:00:58,160 align:start position:0% actually distribute this with two distinct first</c> 00:00:58,160 --> 00:00:58,170 align:start position:0% distinct user interfaces and the first 00:00:58,170 --> 00:01:00,260 align:start position:0% distinct user interfaces and the first one we</c> 00:01:00,260 --> 00:01:00,270 align:start position:0% one is the graphical user interface we 00:01:00,270 --> 00:01:02,779 align:start position:0% one is the graphical user interface we call also</c> 00:01:02,779 --> 00:01:02,789 align:start position:0% call that Omega X and it's also 00:01:02,789 --> 00:01:04,399 align:start position:0% call that Omega X and it's also distributed line</c> 00:01:04,399 --> 00:01:04,409 align:start position:0% distributed with a command line 00:01:04,409 --> 00:01:08,000 align:start position:0% distributed with a command line interface we</c> 00:01:08,000 --> 00:01:08,010 align:start position:0% interface we call that mega CC and we 00:01:08,010 --> 00:01:09,469 align:start position:0% interface we call that mega CC and we bundle single</c> 00:01:09,469 --> 00:01:09,479 align:start position:0% bundle these together into a single 00:01:09,479 --> 00:01:12,109 align:start position:0% bundle these together into a single package name</c> 00:01:12,109 --> 00:01:12,119 align:start position:0% package and that's why we use the name 00:01:12,119 --> 00:01:17,300 align:start position:0% package and that's why we use the name mega any</c> 00:01:17,300 --> 00:01:17,310 align:start position:0% mega xcc okay so maybe there's any 00:01:17,310 --> 00:01:20,030 align:start position:0% mega xcc okay so maybe there's any sequence can</c> 00:01:20,030 --> 00:01:20,040 align:start position:0% sequence analyses available users can 00:01:20,040 --> 00:01:21,620 align:start position:0% sequence analyses available users can align an</c> 00:01:21,620 --> 00:01:21,630 align:start position:0% align sequences maybe it has an 00:01:21,630 --> 00:01:23,660 align:start position:0% align sequences maybe it has an implementation W</c> 00:01:23,660 --> 00:01:23,670 align:start position:0% implementation of the cluster all W 00:01:23,670 --> 00:01:26,450 align:start position:0% implementation of the cluster all W algorithm muscle</c> 00:01:26,450 --> 00:01:26,460 align:start position:0% algorithm users can also use the muscle 00:01:26,460 --> 00:01:30,170 align:start position:0% algorithm users can also use the muscle alignment maximum</c> 00:01:30,170 --> 00:01:30,180 align:start position:0% alignment program mega has a maximum 00:01:30,180 --> 00:01:31,730 align:start position:0% alignment program mega has a maximum likelihood selection</c> 00:01:31,730 --> 00:01:31,740 align:start position:0% likelihood based model selection 00:01:31,740 --> 00:01:34,730 align:start position:0% likelihood based model selection analysis different</c> 00:01:34,730 --> 00:01:34,740 align:start position:0% analysis indicated analyzed 24 different 00:01:34,740 --> 00:01:37,700 align:start position:0% analysis indicated analyzed 24 different DMA and</c> 00:01:37,700 --> 00:01:37,710 align:start position:0% DMA models or 56 amino acid models and 00:01:37,710 --> 00:01:40,580 align:start position:0% DMA models or 56 amino acid models and comparative multiple</c> 00:01:40,580 --> 00:01:40,590 align:start position:0% comparative results based on multiple 00:01:40,590 --> 00:01:44,899 align:start position:0% comparative results based on multiple criteria mega</c> 00:01:44,899 --> 00:01:44,909 align:start position:0% criteria for vulajin construction mega 00:01:44,909 --> 00:01:46,969 align:start position:0% criteria for vulajin construction mega implements maximum</c> 00:01:46,969 --> 00:01:46,979 align:start position:0% implements maximum likelihood maximum 00:01:46,979 --> 00:01:49,399 align:start position:0% implements maximum likelihood maximum parsimony minimum</c> 00:01:49,399 --> 00:01:49,409 align:start position:0% parsimony neighbor-joining minimum 00:01:49,409 --> 00:01:53,389 align:start position:0% parsimony neighbor-joining minimum evolution mega</c> 00:01:53,389 --> 00:01:53,399 align:start position:0% evolution and upgma methods with mega 00:01:53,399 --> 00:01:56,209 align:start position:0% evolution and upgma methods with mega you states</c> 00:01:56,209 --> 00:01:56,219 align:start position:0% you can reconstruct ancestral states 00:01:56,219 --> 00:01:57,920 align:start position:0% you can reconstruct ancestral states using maximum</c> 00:01:57,920 --> 00:01:57,930 align:start position:0% using maximum likely their maximum 00:01:57,930 --> 00:02:01,100 align:start position:0% using maximum likely their maximum parsimony clocks</c> 00:02:01,100 --> 00:02:01,110 align:start position:0% parsimony and then for dating the clocks 00:02:01,110 --> 00:02:04,490 align:start position:0% parsimony and then for dating the clocks Omega molecular</c> 00:02:04,490 --> 00:02:04,500 align:start position:0% Omega has a likelihood based molecular 00:02:04,500 --> 00:02:06,679 align:start position:0% Omega has a likelihood based molecular clock several</c> 00:02:06,679 --> 00:02:06,689 align:start position:0% clock test and also there are several 00:02:06,689 --> 00:02:09,380 align:start position:0% clock test and also there are several ways the</c> 00:02:09,380 --> 00:02:09,390 align:start position:0% ways to construct time trees using the 00:02:09,390 --> 00:02:11,170 align:start position:0% ways to construct time trees using the wrong method</c> 00:02:11,170 --> 00:02:11,180 align:start position:0% wrong time method 00:02:11,180 --> 00:02:13,460 align:start position:0% wrong time method okay 25</c> 00:02:13,460 --> 00:02:13,470 align:start position:0% okay so maybe it's been around for 25 00:02:13,470 --> 00:02:16,789 align:start position:0% okay so maybe it's been around for 25 years 1993</c> 00:02:16,789 --> 00:02:16,799 align:start position:0% years when it was first released in 1993 00:02:16,799 --> 00:02:19,100 align:start position:0% years when it was first released in 1993 the evolved</c> 00:02:19,100 --> 00:02:19,110 align:start position:0% the last 25 years it's evolved 00:02:19,110 --> 00:02:21,619 align:start position:0% the last 25 years it's evolved significant new</c> 00:02:21,619 --> 00:02:21,629 align:start position:0% significant significantly added many new 00:02:21,629 --> 00:02:24,949 align:start position:0% significant significantly added many new tools released</c> 00:02:24,949 --> 00:02:24,959 align:start position:0% tools and methods so in 2012 we released 00:02:24,959 --> 00:02:28,819 align:start position:0% tools and methods so in 2012 we released the in</c> 00:02:28,819 --> 00:02:28,829 align:start position:0% the first version of mega CC and then in 00:02:28,829 --> 00:02:30,289 align:start position:0% the first version of mega CC and then in 2016 00:02:30,289 --> 00:02:30,299 align:start position:0% 2016 00:02:30,299 --> 00:02:34,130 align:start position:0% 2016 mega software</c> 00:02:34,130 --> 00:02:34,140 align:start position:0% mega finally became a 64-bit software 00:02:34,140 --> 00:02:37,039 align:start position:0% mega finally became a 64-bit software and CC</c> 00:02:37,039 --> 00:02:37,049 align:start position:0% and in that version he made mega CC 00:02:37,049 --> 00:02:39,680 align:start position:0% and in that version he made mega CC cross-platform point</c> 00:02:39,680 --> 00:02:39,690 align:start position:0% cross-platform so mega CC at that point 00:02:39,690 --> 00:02:42,890 align:start position:0% cross-platform so mega CC at that point can and</c> 00:02:42,890 --> 00:02:42,900 align:start position:0% can run natively on Windows Linux and 00:02:42,900 --> 00:02:45,500 align:start position:0% can run natively on Windows Linux and Mac X</c> 00:02:45,500 --> 00:02:45,510 align:start position:0% Mac OS the current version is a mega X 00:02:45,510 --> 00:02:49,009 align:start position:0% Mac OS the current version is a mega X which so</c> 00:02:49,009 --> 00:02:49,019 align:start position:0% which we just released this year and so 00:02:49,019 --> 00:02:51,110 align:start position:0% which we just released this year and so the the</c> 00:02:51,110 --> 00:02:51,120 align:start position:0% the mega computational core that's the 00:02:51,120 --> 00:02:53,210 align:start position:0% the mega computational core that's the calculation handles</c> 00:02:53,210 --> 00:02:53,220 align:start position:0% calculation engine and mega it handles 00:02:53,220 --> 00:02:55,130 align:start position:0% calculation engine and mega it handles all computing</c> 00:02:55,130 --> 00:02:55,140 align:start position:0% all the tree searching computing 00:02:55,140 --> 00:02:57,699 align:start position:0% all the tree searching computing distances forth</c> 00:02:57,699 --> 00:02:57,709 align:start position:0% distances branch lengths and so forth 00:02:57,709 --> 00:03:00,759 align:start position:0% distances branch lengths and so forth and and</c> 00:03:00,759 --> 00:03:00,769 align:start position:0% and as a user command-line interface and 00:03:00,769 --> 00:03:02,930 align:start position:0% and as a user command-line interface and so its</c> 00:03:02,930 --> 00:03:02,940 align:start position:0% so Omega is widely known for its 00:03:02,940 --> 00:03:04,460 align:start position:0% so Omega is widely known for its graphical some</c> 00:03:04,460 --> 00:03:04,470 align:start position:0% graphical user interface but in some 00:03:04,470 --> 00:03:06,229 align:start position:0% graphical user interface but in some situations use</c> 00:03:06,229 --> 00:03:06,239 align:start position:0% situations it can be cumbersome to use 00:03:06,239 --> 00:03:08,180 align:start position:0% situations it can be cumbersome to use if or</c> 00:03:08,180 --> 00:03:08,190 align:start position:0% if you have a lot of data files or 00:03:08,190 --> 00:03:12,440 align:start position:0% if you have a lot of data files or people analysis</c> 00:03:12,440 --> 00:03:12,450 align:start position:0% people on to use mega and analysis 00:03:12,450 --> 00:03:14,599 align:start position:0% people on to use mega and analysis pipeline really</c> 00:03:14,599 --> 00:03:14,609 align:start position:0% pipeline the GUI just doesn't really 00:03:14,609 --> 00:03:16,190 align:start position:0% pipeline the GUI just doesn't really work this</c> 00:03:16,190 --> 00:03:16,200 align:start position:0% work well so we took provide this 00:03:16,200 --> 00:03:19,610 align:start position:0% work well so we took provide this command-line is</c> 00:03:19,610 --> 00:03:19,620 align:start position:0% command-line interface and this is 00:03:19,620 --> 00:03:21,440 align:start position:0% command-line interface and this is optimized processing</c> 00:03:21,440 --> 00:03:21,450 align:start position:0% optimized for batch processing 00:03:21,450 --> 00:03:24,080 align:start position:0% optimized for batch processing automation pipelines</c> 00:03:24,080 --> 00:03:24,090 align:start position:0% automation if you're using it pipelines 00:03:24,090 --> 00:03:26,750 align:start position:0% automation if you're using it pipelines and easily</c> 00:03:26,750 --> 00:03:26,760 align:start position:0% and workflow integration and it's easily 00:03:26,760 --> 00:03:28,430 align:start position:0% and workflow integration and it's easily called run</c> 00:03:28,430 --> 00:03:28,440 align:start position:0% called from a command line you can run 00:03:28,440 --> 00:03:30,710 align:start position:0% called from a command line you can run it from</c> 00:03:30,710 --> 00:03:30,720 align:start position:0% it from scripts or running legacy C from 00:03:30,720 --> 00:03:34,509 align:start position:0% it from scripts or running legacy C from other applications</c> 00:03:34,509 --> 00:03:34,519 align:start position:0% 00:03:34,519 --> 00:03:37,940 align:start position:0% alright different</c> 00:03:37,940 --> 00:03:37,950 align:start position:0% alright so mega C C requires different 00:03:37,950 --> 00:03:39,439 align:start position:0% alright so mega C C requires different kinds and</c> 00:03:39,439 --> 00:03:39,449 align:start position:0% kinds of input files will try and 00:03:39,449 --> 00:03:42,559 align:start position:0% kinds of input files will try and support molecular</c> 00:03:42,559 --> 00:03:42,569 align:start position:0% support standard format molecular 00:03:42,569 --> 00:03:44,930 align:start position:0% support standard format molecular sequence FASTA</c> 00:03:44,930 --> 00:03:44,940 align:start position:0% sequence data you can use mega or FASTA 00:03:44,940 --> 00:03:47,720 align:start position:0% sequence data you can use mega or FASTA format mega</c> 00:03:47,720 --> 00:03:47,730 align:start position:0% format there's some analyses in mega 00:03:47,730 --> 00:03:50,689 align:start position:0% format there's some analyses in mega that matrices</c> 00:03:50,689 --> 00:03:50,699 align:start position:0% that you can use for distance matrices 00:03:50,699 --> 00:03:52,580 align:start position:0% that you can use for distance matrices and to</c> 00:03:52,580 --> 00:03:52,590 align:start position:0% and these have the input files have to 00:03:52,590 --> 00:03:55,849 align:start position:0% and these have the input files have to be tree</c> 00:03:55,849 --> 00:03:55,859 align:start position:0% be in the mega format all input tree 00:03:55,859 --> 00:03:57,650 align:start position:0% be in the mega format all input tree files file</c> 00:03:57,650 --> 00:03:57,660 align:start position:0% files need to be in the million file 00:03:57,660 --> 00:04:01,119 align:start position:0% files need to be in the million file format custom</c> 00:04:01,119 --> 00:04:01,129 align:start position:0% format and then there's several custom 00:04:01,129 --> 00:04:04,039 align:start position:0% format and then there's several custom analysis users</c> 00:04:04,039 --> 00:04:04,049 align:start position:0% analysis specific files of mega users 00:04:04,049 --> 00:04:06,369 align:start position:0% analysis specific files of mega users for analysis</c> 00:04:06,369 --> 00:04:06,379 align:start position:0% for instance for the real-time analysis 00:04:06,379 --> 00:04:08,750 align:start position:0% for instance for the real-time analysis calibrations defined</c> 00:04:08,750 --> 00:04:08,760 align:start position:0% calibrations and groups can be defined 00:04:08,760 --> 00:04:13,309 align:start position:0% calibrations and groups can be defined in finally</c> 00:04:13,309 --> 00:04:13,319 align:start position:0% in custom formatted files and finally 00:04:13,319 --> 00:04:14,900 align:start position:0% in custom formatted files and finally there's that's</c> 00:04:14,900 --> 00:04:14,910 align:start position:0% there's a very important file that's 00:04:14,910 --> 00:04:16,729 align:start position:0% there's a very important file that's used mega</c> 00:04:16,729 --> 00:04:16,739 align:start position:0% used in mega CC it's called the mega 00:04:16,739 --> 00:04:19,459 align:start position:0% used in mega CC it's called the mega analysis there</c> 00:04:19,459 --> 00:04:19,469 align:start position:0% analysis options file and that is there 00:04:19,469 --> 00:04:21,170 align:start position:0% analysis options file and that is there some we'll</c> 00:04:21,170 --> 00:04:21,180 align:start position:0% some special considerations so we'll 00:04:21,180 --> 00:04:23,440 align:start position:0% some special considerations so we'll talk now</c> 00:04:23,440 --> 00:04:23,450 align:start position:0% talk about that a bit now 00:04:23,450 --> 00:04:25,840 align:start position:0% talk about that a bit now so a</c> 00:04:25,840 --> 00:04:25,850 align:start position:0% so the mega analysis options file is a 00:04:25,850 --> 00:04:29,470 align:start position:0% so the mega analysis options file is a text exactly</c> 00:04:29,470 --> 00:04:29,480 align:start position:0% text file and it tells mega CC exactly 00:04:29,480 --> 00:04:32,530 align:start position:0% text file and it tells mega CC exactly what it</c> 00:04:32,530 --> 00:04:32,540 align:start position:0% what to do and how to do it and so it 00:04:32,540 --> 00:04:35,200 align:start position:0% what to do and how to do it and so it specifies that</c> 00:04:35,200 --> 00:04:35,210 align:start position:0% specifies all the analysis options that 00:04:35,210 --> 00:04:37,480 align:start position:0% specifies all the analysis options that should for</c> 00:04:37,480 --> 00:04:37,490 align:start position:0% should be used for given calculation for 00:04:37,490 --> 00:04:39,670 align:start position:0% should be used for given calculation for instance a</c> 00:04:39,670 --> 00:04:39,680 align:start position:0% instance with substitution type to use a 00:04:39,680 --> 00:04:42,790 align:start position:0% instance with substitution type to use a model is</c> 00:04:42,790 --> 00:04:42,800 align:start position:0% model or method and this file is 00:04:42,800 --> 00:04:44,920 align:start position:0% model or method and this file is required are</c> 00:04:44,920 --> 00:04:44,930 align:start position:0% required for all calculations that are 00:04:44,930 --> 00:04:50,590 align:start position:0% required for all calculations that are not set</c> 00:04:50,590 --> 00:04:50,600 align:start position:0% not using mega CC we do not allow to set 00:04:50,600 --> 00:04:52,690 align:start position:0% not using mega CC we do not allow to set analysis command-line</c> 00:04:52,690 --> 00:04:52,700 align:start position:0% analysis settings by a command-line 00:04:52,700 --> 00:04:55,870 align:start position:0% analysis settings by a command-line parameters be</c> 00:04:55,870 --> 00:04:55,880 align:start position:0% parameters this file needs to be 00:04:55,880 --> 00:04:57,310 align:start position:0% parameters this file needs to be generated user</c> 00:04:57,310 --> 00:04:57,320 align:start position:0% generated using the graphical user 00:04:57,320 --> 00:05:01,150 align:start position:0% generated using the graphical user interface created</c> 00:05:01,150 --> 00:05:01,160 align:start position:0% interface it should never be created 00:05:01,160 --> 00:05:03,000 align:start position:0% interface it should never be created manually and</c> 00:05:03,000 --> 00:05:03,010 align:start position:0% manually and should never be edited and 00:05:03,010 --> 00:05:06,070 align:start position:0% manually and should never be edited and the graphical</c> 00:05:06,070 --> 00:05:06,080 align:start position:0% the reason we require that the graphical 00:05:06,080 --> 00:05:08,410 align:start position:0% the reason we require that the graphical user to</c> 00:05:08,410 --> 00:05:08,420 align:start position:0% user interface is used is in order to 00:05:08,420 --> 00:05:12,850 align:start position:0% user interface is used is in order to prevent files</c> 00:05:12,850 --> 00:05:12,860 align:start position:0% prevent errors and so how do these files 00:05:12,860 --> 00:05:15,820 align:start position:0% prevent errors and so how do these files prevent that</c> 00:05:15,820 --> 00:05:15,830 align:start position:0% prevent errors so let's assume that 00:05:15,830 --> 00:05:18,280 align:start position:0% prevent errors so let's assume that Megan alignment</c> 00:05:18,280 --> 00:05:18,290 align:start position:0% Megan I've opened a sequence alignment 00:05:18,290 --> 00:05:21,760 align:start position:0% Megan I've opened a sequence alignment of a</c> 00:05:21,760 --> 00:05:21,770 align:start position:0% of coding data and I want to perform a 00:05:21,770 --> 00:05:25,210 align:start position:0% of coding data and I want to perform a maximum I</c> 00:05:25,210 --> 00:05:25,220 align:start position:0% maximum likelihood tree search so when I 00:05:25,220 --> 00:05:27,190 align:start position:0% maximum likelihood tree search so when I launch analysis</c> 00:05:27,190 --> 00:05:27,200 align:start position:0% launch that calculation the analysis 00:05:27,200 --> 00:05:29,050 align:start position:0% launch that calculation the analysis preference up</c> 00:05:29,050 --> 00:05:29,060 align:start position:0% preference is dialog to be opened up 00:05:29,060 --> 00:05:31,800 align:start position:0% preference is dialog to be opened up with here</c> 00:05:31,800 --> 00:05:31,810 align:start position:0% with default options like we see here 00:05:31,810 --> 00:05:36,490 align:start position:0% with default options like we see here but be</c> 00:05:36,490 --> 00:05:36,500 align:start position:0% but let's say I want my data to be 00:05:36,500 --> 00:05:38,920 align:start position:0% but let's say I want my data to be translated analysis</c> 00:05:38,920 --> 00:05:38,930 align:start position:0% translated before I run this analysis 00:05:38,930 --> 00:05:45,100 align:start position:0% translated before I run this analysis and change</c> 00:05:45,100 --> 00:05:45,110 align:start position:0% and so what I would do is I would change 00:05:45,110 --> 00:05:48,340 align:start position:0% and so what I would do is I would change the nucleotide</c> 00:05:48,340 --> 00:05:48,350 align:start position:0% the the substitution time for nucleotide 00:05:48,350 --> 00:05:51,280 align:start position:0% the the substitution time for nucleotide to a</c> 00:05:51,280 --> 00:05:51,290 align:start position:0% to amino acids and when I did that a 00:05:51,290 --> 00:05:52,480 align:start position:0% to amino acids and when I did that a bunch just</c> 00:05:52,480 --> 00:05:52,490 align:start position:0% bunch of other options would just 00:05:52,490 --> 00:05:55,570 align:start position:0% bunch of other options would just automatically instance</c> 00:05:55,570 --> 00:05:55,580 align:start position:0% automatically change and so for instance 00:05:55,580 --> 00:05:58,420 align:start position:0% automatically change and so for instance a was</c> 00:05:58,420 --> 00:05:58,430 align:start position:0% a genetic code protocol option which was 00:05:58,430 --> 00:06:00,610 align:start position:0% a genetic code protocol option which was disabled we</c> 00:06:00,610 --> 00:06:00,620 align:start position:0% disabled now become enabled because we 00:06:00,620 --> 00:06:02,260 align:start position:0% disabled now become enabled because we need translate</c> 00:06:02,260 --> 00:06:02,270 align:start position:0% need a genetic code table to translate 00:06:02,270 --> 00:06:06,220 align:start position:0% need a genetic code table to translate the change</c> 00:06:06,220 --> 00:06:06,230 align:start position:0% the data and then the model will change 00:06:06,230 --> 00:06:08,530 align:start position:0% the data and then the model will change from an</c> 00:06:08,530 --> 00:06:08,540 align:start position:0% from a nucleotide specific model to an 00:06:08,540 --> 00:06:12,520 align:start position:0% from a nucleotide specific model to an amino finally</c> 00:06:12,520 --> 00:06:12,530 align:start position:0% amino acid specific model and it finally 00:06:12,530 --> 00:06:14,950 align:start position:0% amino acid specific model and it finally be would</c> 00:06:14,950 --> 00:06:14,960 align:start position:0% be select code on positions option would 00:06:14,960 --> 00:06:17,410 align:start position:0% be select code on positions option would become no</c> 00:06:17,410 --> 00:06:17,420 align:start position:0% become disabled because if it would no 00:06:17,420 --> 00:06:20,470 align:start position:0% become disabled because if it would no longer these</c> 00:06:20,470 --> 00:06:20,480 align:start position:0% longer be relevant and so setting these 00:06:20,480 --> 00:06:23,800 align:start position:0% longer be relevant and so setting these options a</c> 00:06:23,800 --> 00:06:23,810 align:start position:0% options or given analysis metadata is a 00:06:23,810 --> 00:06:25,480 align:start position:0% options or given analysis metadata is a complex are</c> 00:06:25,480 --> 00:06:25,490 align:start position:0% complex thing because the options are 00:06:25,490 --> 00:06:28,450 align:start position:0% complex thing because the options are context our</c> 00:06:28,450 --> 00:06:28,460 align:start position:0% context sensitive and if we allow to our 00:06:28,460 --> 00:06:30,580 align:start position:0% context sensitive and if we allow to our ask by</c> 00:06:30,580 --> 00:06:30,590 align:start position:0% ask users to provide these options by 00:06:30,590 --> 00:06:32,200 align:start position:0% ask users to provide these options by command highly</c> 00:06:32,200 --> 00:06:32,210 align:start position:0% command line it would be highly 00:06:32,210 --> 00:06:35,760 align:start position:0% command line it would be highly error-prone 00:06:35,760 --> 00:06:35,770 align:start position:0% 00:06:35,770 --> 00:06:40,230 align:start position:0% so output</c> 00:06:40,230 --> 00:06:40,240 align:start position:0% so when ever mega produces its output 00:06:40,240 --> 00:06:41,850 align:start position:0% so when ever mega produces its output result standard</c> 00:06:41,850 --> 00:06:41,860 align:start position:0% result files we try and use standard 00:06:41,860 --> 00:06:43,350 align:start position:0% result files we try and use standard formats easy</c> 00:06:43,350 --> 00:06:43,360 align:start position:0% formats that are easy to parse and easy 00:06:43,360 --> 00:06:46,379 align:start position:0% formats that are easy to parse and easy to for</c> 00:06:46,379 --> 00:06:46,389 align:start position:0% to work with an analysis pipelines for 00:06:46,389 --> 00:06:47,430 align:start position:0% to work with an analysis pipelines for sequence data</c> 00:06:47,430 --> 00:06:47,440 align:start position:0% sequence data 00:06:47,440 --> 00:06:50,309 align:start position:0% sequence data the format</c> 00:06:50,309 --> 00:06:50,319 align:start position:0% the default is to output my mega format 00:06:50,319 --> 00:06:52,080 align:start position:0% the default is to output my mega format but format</c> 00:06:52,080 --> 00:06:52,090 align:start position:0% but you can specify the FASTA format 00:06:52,090 --> 00:06:55,620 align:start position:0% but you can specify the FASTA format instead using</c> 00:06:55,620 --> 00:06:55,630 align:start position:0% instead trees are always output using 00:06:55,630 --> 00:06:58,830 align:start position:0% instead trees are always output using the the</c> 00:06:58,830 --> 00:06:58,840 align:start position:0% the format there's one exception the 00:06:58,840 --> 00:07:01,100 align:start position:0% the format there's one exception the ground Nexus</c> 00:07:01,100 --> 00:07:01,110 align:start position:0% ground time analysis adds an extra Nexus 00:07:01,110 --> 00:07:06,210 align:start position:0% ground time analysis adds an extra Nexus file most</c> 00:07:06,210 --> 00:07:06,220 align:start position:0% file for the tree and putting with most 00:07:06,220 --> 00:07:08,070 align:start position:0% file for the tree and putting with most other the</c> 00:07:08,070 --> 00:07:08,080 align:start position:0% other results or output in the 00:07:08,080 --> 00:07:12,089 align:start position:0% other results or output in the comma-separated then</c> 00:07:12,089 --> 00:07:12,099 align:start position:0% comma-separated values format and then 00:07:12,099 --> 00:07:13,589 align:start position:0% comma-separated values format and then finally that's</c> 00:07:13,589 --> 00:07:13,599 align:start position:0% finally for every calculation that's 00:07:13,599 --> 00:07:16,040 align:start position:0% finally for every calculation that's running file</c> 00:07:16,040 --> 00:07:16,050 align:start position:0% running mega CC we output a summary file 00:07:16,050 --> 00:07:18,719 align:start position:0% running mega CC we output a summary file this values</c> 00:07:18,719 --> 00:07:18,729 align:start position:0% this file contains calculated values 00:07:18,729 --> 00:07:20,100 align:start position:0% this file contains calculated values that output</c> 00:07:20,100 --> 00:07:20,110 align:start position:0% that cannot be added to standard output 00:07:20,110 --> 00:07:23,219 align:start position:0% that cannot be added to standard output formats for</c> 00:07:23,219 --> 00:07:23,229 align:start position:0% formats or should not for instance for 00:07:23,229 --> 00:07:25,350 align:start position:0% formats or should not for instance for the a</c> 00:07:25,350 --> 00:07:25,360 align:start position:0% the likelihood tree search we computed a 00:07:25,360 --> 00:07:27,029 align:start position:0% the likelihood tree search we computed a long them</c> 00:07:27,029 --> 00:07:27,039 align:start position:0% long likelihood value in them 00:07:27,039 --> 00:07:28,499 align:start position:0% long likelihood value in them it unit</c> 00:07:28,499 --> 00:07:28,509 align:start position:0% it doesn't really belong with the unit 00:07:28,509 --> 00:07:30,180 align:start position:0% it doesn't really belong with the unit file summary</c> 00:07:30,180 --> 00:07:30,190 align:start position:0% file so we just put that on a summary 00:07:30,190 --> 00:07:32,879 align:start position:0% file so we just put that on a summary file you</c> 00:07:32,879 --> 00:07:32,889 align:start position:0% file and whenever you run a mega CC you 00:07:32,889 --> 00:07:34,559 align:start position:0% file and whenever you run a mega CC you should for</c> 00:07:34,559 --> 00:07:34,569 align:start position:0% should always check the summary file for 00:07:34,569 --> 00:07:36,089 align:start position:0% should always check the summary file for any that's</c> 00:07:36,089 --> 00:07:36,099 align:start position:0% any warnings or errors because that's 00:07:36,099 --> 00:07:39,510 align:start position:0% any warnings or errors because that's where so</c> 00:07:39,510 --> 00:07:39,520 align:start position:0% where a mega CC sked unlock them okay so 00:07:39,520 --> 00:07:43,200 align:start position:0% where a mega CC sked unlock them okay so how bit</c> 00:07:43,200 --> 00:07:43,210 align:start position:0% how to use mega CD so it's a bit 00:07:43,210 --> 00:07:44,339 align:start position:0% how to use mega CD so it's a bit different line</c> 00:07:44,339 --> 00:07:44,349 align:start position:0% different than a lot of command line 00:07:44,349 --> 00:07:46,320 align:start position:0% different than a lot of command line applications open</c> 00:07:46,320 --> 00:07:46,330 align:start position:0% applications first any deals you open 00:07:46,330 --> 00:07:48,450 align:start position:0% applications first any deals you open the set</c> 00:07:48,450 --> 00:07:48,460 align:start position:0% the graphical user interface you can set 00:07:48,460 --> 00:07:51,540 align:start position:0% the graphical user interface you can set it and</c> 00:07:51,540 --> 00:07:51,550 align:start position:0% it in prototype model in a specified and 00:07:51,550 --> 00:07:52,920 align:start position:0% it in prototype model in a specified and input be</c> 00:07:52,920 --> 00:07:52,930 align:start position:0% input data type that's going to be 00:07:52,930 --> 00:07:56,270 align:start position:0% input data type that's going to be operated analysis</c> 00:07:56,270 --> 00:07:56,280 align:start position:0% operated on then a selecting analysis 00:07:56,280 --> 00:08:00,510 align:start position:0% operated on then a selecting analysis select save</c> 00:08:00,510 --> 00:08:00,520 align:start position:0% select the settings to you going to save 00:08:00,520 --> 00:08:03,209 align:start position:0% select the settings to you going to save that and</c> 00:08:03,209 --> 00:08:03,219 align:start position:0% that mega t'v analysis options file and 00:08:03,219 --> 00:08:07,080 align:start position:0% that mega t'v analysis options file and then to</c> 00:08:07,080 --> 00:08:07,090 align:start position:0% then launch the analysis okay now to 00:08:07,090 --> 00:08:09,689 align:start position:0% then launch the analysis okay now to illustrate an</c> 00:08:09,689 --> 00:08:09,699 align:start position:0% illustrate this so I walk through an 00:08:09,699 --> 00:08:13,559 align:start position:0% illustrate this so I walk through an example a</c> 00:08:13,559 --> 00:08:13,569 align:start position:0% example of using mega xcc to generate a 00:08:13,569 --> 00:08:17,779 align:start position:0% example of using mega xcc to generate a time age</c> 00:08:17,779 --> 00:08:17,789 align:start position:0% time tree and so I have a tree of age 00:08:17,789 --> 00:08:20,550 align:start position:0% time tree and so I have a tree of age and title</c> 00:08:20,550 --> 00:08:20,560 align:start position:0% and I want to calculate divergence title 00:08:20,560 --> 00:08:24,270 align:start position:0% and I want to calculate divergence title for I'm</c> 00:08:24,270 --> 00:08:24,280 align:start position:0% for this tree and so the first thing I'm 00:08:24,280 --> 00:08:26,100 align:start position:0% for this tree and so the first thing I'm going the</c> 00:08:26,100 --> 00:08:26,110 align:start position:0% going to do is I'm gonna open up the 00:08:26,110 --> 00:08:28,589 align:start position:0% going to do is I'm gonna open up the graphical to</c> 00:08:28,589 --> 00:08:28,599 align:start position:0% graphical user interface I'm going to 00:08:28,599 --> 00:08:30,120 align:start position:0% graphical user interface I'm going to set do</c> 00:08:30,120 --> 00:08:30,130 align:start position:0% set it in the prototype mode and I do 00:08:30,130 --> 00:08:33,269 align:start position:0% set it in the prototype mode and I do that button</c> 00:08:33,269 --> 00:08:33,279 align:start position:0% that by clicking on the prototype button 00:08:33,279 --> 00:08:34,380 align:start position:0% that by clicking on the prototype button let's right</c> 00:08:34,380 --> 00:08:34,390 align:start position:0% let's down here in the bottom right 00:08:34,390 --> 00:08:38,010 align:start position:0% let's down here in the bottom right corner do</c> 00:08:38,010 --> 00:08:38,020 align:start position:0% corner with the main form and when I do 00:08:38,020 --> 00:08:39,839 align:start position:0% corner with the main form and when I do that going</c> 00:08:39,839 --> 00:08:39,849 align:start position:0% that a dialogues on a pop-up it's going 00:08:39,849 --> 00:08:41,880 align:start position:0% that a dialogues on a pop-up it's going to type</c> 00:08:41,880 --> 00:08:41,890 align:start position:0% to prompt me for the kind of data type 00:08:41,890 --> 00:08:43,290 align:start position:0% to prompt me for the kind of data type that the</c> 00:08:43,290 --> 00:08:43,300 align:start position:0% that I'm going to be using for the 00:08:43,300 --> 00:08:45,540 align:start position:0% that I'm going to be using for the calculation data</c> 00:08:45,540 --> 00:08:45,550 align:start position:0% calculation and you select that data 00:08:45,550 --> 00:08:48,430 align:start position:0% calculation and you select that data type here</c> 00:08:48,430 --> 00:08:48,440 align:start position:0% type from the drop down menu here 00:08:48,440 --> 00:08:51,249 align:start position:0% type from the drop down menu here and any</c> 00:08:51,249 --> 00:08:51,259 align:start position:0% and once he specified that data type any 00:08:51,259 --> 00:08:52,990 align:start position:0% and once he specified that data type any analyses data</c> 00:08:52,990 --> 00:08:53,000 align:start position:0% analyses are not relevant for that data 00:08:53,000 --> 00:08:54,850 align:start position:0% analyses are not relevant for that data type form</c> 00:08:54,850 --> 00:08:54,860 align:start position:0% type become disabled or the minion form 00:08:54,860 --> 00:08:58,980 align:start position:0% type become disabled or the minion form and tree</c> 00:08:58,980 --> 00:08:58,990 align:start position:0% and then I want to compute a time tree 00:08:58,990 --> 00:09:00,850 align:start position:0% and then I want to compute a time tree so to</c> 00:09:00,850 --> 00:09:00,860 align:start position:0% so what I'm going to do is I'm going to 00:09:00,860 --> 00:09:03,220 align:start position:0% so what I'm going to do is I'm going to click compute</c> 00:09:03,220 --> 00:09:03,230 align:start position:0% click on the clocks menu click compute 00:09:03,230 --> 00:09:04,869 align:start position:0% click on the clocks menu click compute time select</c> 00:09:04,869 --> 00:09:04,879 align:start position:0% time tree and then I'm going to select 00:09:04,879 --> 00:09:11,139 align:start position:0% time tree and then I'm going to select the any</c> 00:09:11,139 --> 00:09:11,149 align:start position:0% the real time ml/min deal item and any 00:09:11,149 --> 00:09:14,079 align:start position:0% the real time ml/min deal item and any time the</c> 00:09:14,079 --> 00:09:14,089 align:start position:0% time you launch an analysis in omega the 00:09:14,089 --> 00:09:15,220 align:start position:0% time you launch an analysis in omega the first up</c> 00:09:15,220 --> 00:09:15,230 align:start position:0% first thing we're going to do is open up 00:09:15,230 --> 00:09:18,009 align:start position:0% first thing we're going to do is open up our in</c> 00:09:18,009 --> 00:09:18,019 align:start position:0% our analysis preferences dialog and in 00:09:18,019 --> 00:09:19,900 align:start position:0% our analysis preferences dialog and in this settings</c> 00:09:19,900 --> 00:09:19,910 align:start position:0% this dialog we have all the settings 00:09:19,910 --> 00:09:21,790 align:start position:0% this dialog we have all the settings names right</c> 00:09:21,790 --> 00:09:21,800 align:start position:0% names on this left column on the right 00:09:21,800 --> 00:09:23,110 align:start position:0% names on this left column on the right column to</c> 00:09:23,110 --> 00:09:23,120 align:start position:0% column of the values that are going to 00:09:23,120 --> 00:09:27,400 align:start position:0% column of the values that are going to be here</c> 00:09:27,400 --> 00:09:27,410 align:start position:0% be used and anything in white over here 00:09:27,410 --> 00:09:30,790 align:start position:0% be used and anything in white over here is think</c> 00:09:30,790 --> 00:09:30,800 align:start position:0% is a value that you can edit and I think 00:09:30,800 --> 00:09:31,900 align:start position:0% is a value that you can edit and I think it's do</c> 00:09:31,900 --> 00:09:31,910 align:start position:0% it's a little hard to see so what I do 00:09:31,910 --> 00:09:34,449 align:start position:0% it's a little hard to see so what I do is to</c> 00:09:34,449 --> 00:09:34,459 align:start position:0% is I just put a little red star next to 00:09:34,459 --> 00:09:37,449 align:start position:0% is I just put a little red star next to each read-only</c> 00:09:37,449 --> 00:09:37,459 align:start position:0% each one and anything else is read-only 00:09:37,459 --> 00:09:40,569 align:start position:0% each one and anything else is read-only and just</c> 00:09:40,569 --> 00:09:40,579 align:start position:0% and the way you enter value you just 00:09:40,579 --> 00:09:44,319 align:start position:0% and the way you enter value you just click an</c> 00:09:44,319 --> 00:09:44,329 align:start position:0% click on that white like box and an 00:09:44,329 --> 00:09:46,869 align:start position:0% click on that white like box and an editor a</c> 00:09:46,869 --> 00:09:46,879 align:start position:0% editor will open up either like a 00:09:46,879 --> 00:09:49,030 align:start position:0% editor will open up either like a drop-down a</c> 00:09:49,030 --> 00:09:49,040 align:start position:0% drop-down list or a spinner be a 00:09:49,040 --> 00:09:54,699 align:start position:0% drop-down list or a spinner be a checkbox finished</c> 00:09:54,699 --> 00:09:54,709 align:start position:0% checkbox and then once you're finished 00:09:54,709 --> 00:09:56,590 align:start position:0% checkbox and then once you're finished selecting to</c> 00:09:56,590 --> 00:09:56,600 align:start position:0% selecting the options that you want to 00:09:56,600 --> 00:09:59,850 align:start position:0% selecting the options that you want to use and</c> 00:09:59,850 --> 00:09:59,860 align:start position:0% use click the Save Settings button and 00:09:59,860 --> 00:10:02,499 align:start position:0% use click the Save Settings button and we're my</c> 00:10:02,499 --> 00:10:02,509 align:start position:0% we're going to save this to a dotting my 00:10:02,509 --> 00:10:05,230 align:start position:0% we're going to save this to a dotting my own to</c> 00:10:05,230 --> 00:10:05,240 align:start position:0% own file and so make it is going to 00:10:05,240 --> 00:10:08,530 align:start position:0% own file and so make it is going to propose this</c> 00:10:08,530 --> 00:10:08,540 align:start position:0% propose a meaningful filename in this 00:10:08,540 --> 00:10:10,269 align:start position:0% propose a meaningful filename in this case that</c> 00:10:10,269 --> 00:10:10,279 align:start position:0% case it's real time ml nucleotide that 00:10:10,279 --> 00:10:12,970 align:start position:0% case it's real time ml nucleotide that mal you</c> 00:10:12,970 --> 00:10:12,980 align:start position:0% mal so real time is de method that's you 00:10:12,980 --> 00:10:15,550 align:start position:0% mal so real time is de method that's you or analysis</c> 00:10:15,550 --> 00:10:15,560 align:start position:0% or the analysis we're running analysis 00:10:15,560 --> 00:10:16,870 align:start position:0% or the analysis we're running analysis for method</c> 00:10:16,870 --> 00:10:16,880 align:start position:0% for maximum likelihood of the method 00:10:16,880 --> 00:10:18,850 align:start position:0% for maximum likelihood of the method you're data</c> 00:10:18,850 --> 00:10:18,860 align:start position:0% you're using I chose a nucleotide data 00:10:18,860 --> 00:10:21,670 align:start position:0% you're using I chose a nucleotide data for convention</c> 00:10:21,670 --> 00:10:21,680 align:start position:0% for this and so that made me convention 00:10:21,680 --> 00:10:23,170 align:start position:0% for this and so that made me convention can your</c> 00:10:23,170 --> 00:10:23,180 align:start position:0% can be useful for keeping your head your 00:10:23,180 --> 00:10:24,639 align:start position:0% can be useful for keeping your head your files name</c> 00:10:24,639 --> 00:10:24,649 align:start position:0% files organized you can give it any name 00:10:24,649 --> 00:10:26,860 align:start position:0% files organized you can give it any name you file</c> 00:10:26,860 --> 00:10:26,870 align:start position:0% you want just keep the audio file 00:10:26,870 --> 00:10:31,480 align:start position:0% you want just keep the audio file extension real-time</c> 00:10:31,480 --> 00:10:31,490 align:start position:0% extension ok so now for this real-time 00:10:31,490 --> 00:10:32,549 align:start position:0% extension ok so now for this real-time analysis 00:10:32,549 --> 00:10:32,559 align:start position:0% analysis 00:10:32,559 --> 00:10:34,749 align:start position:0% analysis there's are</c> 00:10:34,749 --> 00:10:34,759 align:start position:0% there's several input files that are 00:10:34,759 --> 00:10:36,999 align:start position:0% there's several input files that are required file</c> 00:10:36,999 --> 00:10:37,009 align:start position:0% required negative Alice's options file 00:10:37,009 --> 00:10:39,400 align:start position:0% required negative Alice's options file is we'll</c> 00:10:39,400 --> 00:10:39,410 align:start position:0% is required for every calculation we'll 00:10:39,410 --> 00:10:42,009 align:start position:0% is required for every calculation we'll be going</c> 00:10:42,009 --> 00:10:42,019 align:start position:0% be using the agency C we're also going 00:10:42,019 --> 00:10:45,460 align:start position:0% be using the agency C we're also going to tree</c> 00:10:45,460 --> 00:10:45,470 align:start position:0% to need a sequence alignment a good tree 00:10:45,470 --> 00:10:48,220 align:start position:0% to need a sequence alignment a good tree file out-group</c> 00:10:48,220 --> 00:10:48,230 align:start position:0% file we're going to use an out-group 00:10:48,230 --> 00:10:50,259 align:start position:0% file we're going to use an out-group file tree</c> 00:10:50,259 --> 00:10:50,269 align:start position:0% file to define the out-group of the tree 00:10:50,269 --> 00:10:54,100 align:start position:0% file to define the out-group of the tree and file</c> 00:10:54,100 --> 00:10:54,110 align:start position:0% and there's an optional calibration file 00:10:54,110 --> 00:10:56,740 align:start position:0% and there's an optional calibration file where time</c> 00:10:56,740 --> 00:10:56,750 align:start position:0% where we can supply that versions time 00:10:56,750 --> 00:10:58,329 align:start position:0% where we can supply that versions time calibration going</c> 00:10:58,329 --> 00:10:58,339 align:start position:0% calibration constraints that we're going 00:10:58,339 --> 00:11:01,150 align:start position:0% calibration constraints that we're going to first</c> 00:11:01,150 --> 00:11:01,160 align:start position:0% to use that as well so I think the first 00:11:01,160 --> 00:11:01,510 align:start position:0% to use that as well so I think the first three 00:11:01,510 --> 00:11:01,520 align:start position:0% three 00:11:01,520 --> 00:11:04,060 align:start position:0% three files are</c> 00:11:04,060 --> 00:11:04,070 align:start position:0% files I think we understand with the are 00:11:04,070 --> 00:11:05,470 align:start position:0% files I think we understand with the are these go</c> 00:11:05,470 --> 00:11:05,480 align:start position:0% these last two let me just quickly go 00:11:05,480 --> 00:11:07,780 align:start position:0% these last two let me just quickly go over for</c> 00:11:07,780 --> 00:11:07,790 align:start position:0% over the format that's required for 00:11:07,790 --> 00:11:11,620 align:start position:0% over the format that's required for those output</c> 00:11:11,620 --> 00:11:11,630 align:start position:0% those files and so to specify the output 00:11:11,630 --> 00:11:13,330 align:start position:0% those files and so to specify the output we actually</c> 00:11:13,330 --> 00:11:13,340 align:start position:0% we can use a text file there's actually 00:11:13,340 --> 00:11:15,190 align:start position:0% we can use a text file there's actually two is</c> 00:11:15,190 --> 00:11:15,200 align:start position:0% two options to do this the first one is 00:11:15,200 --> 00:11:17,320 align:start position:0% two options to do this the first one is to I</c> 00:11:17,320 --> 00:11:17,330 align:start position:0% to use a text file and so let's say I 00:11:17,330 --> 00:11:19,060 align:start position:0% to use a text file and so let's say I created called</c> 00:11:19,060 --> 00:11:19,070 align:start position:0% created a text file and it's called 00:11:19,070 --> 00:11:23,350 align:start position:0% created a text file and it's called outgrew want</c> 00:11:23,350 --> 00:11:23,360 align:start position:0% outgrew txt and meaning that file I want 00:11:23,360 --> 00:11:24,790 align:start position:0% outgrew txt and meaning that file I want to going</c> 00:11:24,790 --> 00:11:24,800 align:start position:0% to specify the out-group and I'm going 00:11:24,800 --> 00:11:27,250 align:start position:0% to specify the out-group and I'm going to group</c> 00:11:27,250 --> 00:11:27,260 align:start position:0% to use a format taxon name equals group 00:11:27,260 --> 00:11:29,710 align:start position:0% to use a format taxon name equals group name but</c> 00:11:29,710 --> 00:11:29,720 align:start position:0% name and so what I just drag but 00:11:29,720 --> 00:11:31,990 align:start position:0% name and so what I just drag but aligning is</c> 00:11:31,990 --> 00:11:32,000 align:start position:0% aligning that file light out group is 00:11:32,000 --> 00:11:34,030 align:start position:0% aligning that file light out group is going given</c> 00:11:34,030 --> 00:11:34,040 align:start position:0% going to be given and I just had given 00:11:34,040 --> 00:11:36,930 align:start position:0% going to be given and I just had given equals uh</c> 00:11:36,930 --> 00:11:36,940 align:start position:0% equals output and now group can have uh 00:11:36,940 --> 00:11:40,720 align:start position:0% equals output and now group can have uh you there</c> 00:11:40,720 --> 00:11:40,730 align:start position:0% you know more than one sequence in there 00:11:40,730 --> 00:11:43,090 align:start position:0% you know more than one sequence in there that's have</c> 00:11:43,090 --> 00:11:43,100 align:start position:0% that's fine in my example I just have 00:11:43,100 --> 00:11:47,140 align:start position:0% that's fine in my example I just have one the</c> 00:11:47,140 --> 00:11:47,150 align:start position:0% one another option to specify the 00:11:47,150 --> 00:11:49,050 align:start position:0% one another option to specify the out-group that</c> 00:11:49,050 --> 00:11:49,060 align:start position:0% out-group products that abusing that 00:11:49,060 --> 00:11:51,280 align:start position:0% out-group products that abusing that specify that</c> 00:11:51,280 --> 00:11:51,290 align:start position:0% specify the output Pacific using that 00:11:51,290 --> 00:11:53,680 align:start position:0% specify the output Pacific using that file mega</c> 00:11:53,680 --> 00:11:53,690 align:start position:0% file we can actually define it in a mega 00:11:53,690 --> 00:11:56,950 align:start position:0% file we can actually define it in a mega formatted so</c> 00:11:56,950 --> 00:11:56,960 align:start position:0% formatted sequence alignment file and so 00:11:56,960 --> 00:11:59,620 align:start position:0% formatted sequence alignment file and so my this</c> 00:11:59,620 --> 00:11:59,630 align:start position:0% my like sequence line the file for this 00:11:59,630 --> 00:12:03,940 align:start position:0% my like sequence line the file for this is a</c> 00:12:03,940 --> 00:12:03,950 align:start position:0% is going to be empty cDNA and that's a 00:12:03,950 --> 00:12:07,060 align:start position:0% is going to be empty cDNA and that's a mega I</c> 00:12:07,060 --> 00:12:07,070 align:start position:0% mega formatted file and in that file I 00:12:07,070 --> 00:12:09,720 align:start position:0% mega formatted file and in that file I can property</c> 00:12:09,720 --> 00:12:09,730 align:start position:0% can use what we call the group property 00:12:09,730 --> 00:12:14,110 align:start position:0% can use what we call the group property right given</c> 00:12:14,110 --> 00:12:14,120 align:start position:0% right here to specify that a given 00:12:14,120 --> 00:12:16,540 align:start position:0% right here to specify that a given sequence way</c> 00:12:16,540 --> 00:12:16,550 align:start position:0% sequence belongs to a group and the way 00:12:16,550 --> 00:12:19,090 align:start position:0% sequence belongs to a group and the way I our</c> 00:12:19,090 --> 00:12:19,100 align:start position:0% I do that is the format is we have our 00:12:19,100 --> 00:12:21,700 align:start position:0% I do that is the format is we have our pound do</c> 00:12:21,700 --> 00:12:21,710 align:start position:0% pound sign that our taxonomy what we do 00:12:21,710 --> 00:12:23,440 align:start position:0% pound sign that our taxonomy what we do is and</c> 00:12:23,440 --> 00:12:23,450 align:start position:0% is append to that we say underscore and 00:12:23,450 --> 00:12:26,800 align:start position:0% is append to that we say underscore and embraces this</c> 00:12:26,800 --> 00:12:26,810 align:start position:0% embraces we write a group name for this 00:12:26,810 --> 00:12:28,360 align:start position:0% embraces we write a group name for this example just</c> 00:12:28,360 --> 00:12:28,370 align:start position:0% example we need an algorithm we're just 00:12:28,370 --> 00:12:30,160 align:start position:0% example we need an algorithm we're just going this</c> 00:12:30,160 --> 00:12:30,170 align:start position:0% going to call it out gluten and so this 00:12:30,170 --> 00:12:31,480 align:start position:0% going to call it out gluten and so this is Omega</c> 00:12:31,480 --> 00:12:31,490 align:start position:0% is what it looks like in the Omega 00:12:31,490 --> 00:12:36,550 align:start position:0% is what it looks like in the Omega sequence the</c> 00:12:36,550 --> 00:12:36,560 align:start position:0% sequence environment file here and the 00:12:36,560 --> 00:12:39,070 align:start position:0% sequence environment file here and the other a</c> 00:12:39,070 --> 00:12:39,080 align:start position:0% other file we're going to use its a 00:12:39,080 --> 00:12:43,120 align:start position:0% other file we're going to use its a calibration what</c> 00:12:43,120 --> 00:12:43,130 align:start position:0% calibration scan chains file and what 00:12:43,130 --> 00:12:45,330 align:start position:0% calibration scan chains file and what were provide</c> 00:12:45,330 --> 00:12:45,340 align:start position:0% were you gonna do is we provide 00:12:45,340 --> 00:12:48,010 align:start position:0% were you gonna do is we provide divergence constraints</c> 00:12:48,010 --> 00:12:48,020 align:start position:0% divergence times calibration constraints 00:12:48,020 --> 00:12:51,400 align:start position:0% divergence times calibration constraints for I</c> 00:12:51,400 --> 00:12:51,410 align:start position:0% for two nodes in our tree and this is I 00:12:51,410 --> 00:12:53,920 align:start position:0% for two nodes in our tree and this is I have I</c> 00:12:53,920 --> 00:12:53,930 align:start position:0% have a calibration txt text file that I 00:12:53,930 --> 00:12:55,810 align:start position:0% have a calibration txt text file that I created that</c> 00:12:55,810 --> 00:12:55,820 align:start position:0% created and this is the contents of that 00:12:55,820 --> 00:12:58,900 align:start position:0% created and this is the contents of that file I'm</c> 00:12:58,900 --> 00:12:58,910 align:start position:0% file right here I have two lines I'm 00:12:58,910 --> 00:13:00,640 align:start position:0% file right here I have two lines I'm specifying using</c> 00:13:00,640 --> 00:13:00,650 align:start position:0% specifying two constraints they're using 00:13:00,650 --> 00:13:03,160 align:start position:0% specifying two constraints they're using different line</c> 00:13:03,160 --> 00:13:03,170 align:start position:0% different formats and in the first line 00:13:03,170 --> 00:13:05,200 align:start position:0% different formats and in the first line this do</c> 00:13:05,200 --> 00:13:05,210 align:start position:0% this is maybe first method we can do 00:13:05,210 --> 00:13:09,370 align:start position:0% this is maybe first method we can do this specify</c> 00:13:09,370 --> 00:13:09,380 align:start position:0% this and that meant that is to specify 00:13:09,380 --> 00:13:12,360 align:start position:0% this and that meant that is to specify two common</c> 00:13:12,360 --> 00:13:12,370 align:start position:0% two taxa whose most recent common 00:13:12,370 --> 00:13:15,450 align:start position:0% two taxa whose most recent common sister that</c> 00:13:15,450 --> 00:13:15,460 align:start position:0% sister is the node in the tree that 00:13:15,460 --> 00:13:17,160 align:start position:0% sister is the node in the tree that we're to</c> 00:13:17,160 --> 00:13:17,170 align:start position:0% we're going to apply this calibration to 00:13:17,170 --> 00:13:20,550 align:start position:0% we're going to apply this calibration to so want</c> 00:13:20,550 --> 00:13:20,560 align:start position:0% so in this example I've said that I want 00:13:20,560 --> 00:13:22,079 align:start position:0% so in this example I've said that I want the for</c> 00:13:22,079 --> 00:13:22,089 align:start position:0% the most recent common ancestor for 00:13:22,089 --> 00:13:25,019 align:start position:0% the most recent common ancestor for chimpanzee like</c> 00:13:25,019 --> 00:13:25,029 align:start position:0% chimpanzee I bought a boat and like 00:13:25,029 --> 00:13:27,420 align:start position:0% chimpanzee I bought a boat and like minimum 2.4</c> 00:13:27,420 --> 00:13:27,430 align:start position:0% minimum divergence time I had like 2.4 00:13:27,430 --> 00:13:29,579 align:start position:0% minimum divergence time I had like 2.4 million key</c> 00:13:29,579 --> 00:13:29,589 align:start position:0% million years in the next time I key 00:13:29,589 --> 00:13:35,579 align:start position:0% million years in the next time I key point use</c> 00:13:35,579 --> 00:13:35,589 align:start position:0% point 2 now the second method I can use 00:13:35,589 --> 00:13:39,720 align:start position:0% point 2 now the second method I can use is using</c> 00:13:39,720 --> 00:13:39,730 align:start position:0% is to specify a know to calibrate using 00:13:39,730 --> 00:13:42,390 align:start position:0% is to specify a know to calibrate using a labeled</c> 00:13:42,390 --> 00:13:42,400 align:start position:0% a label alone and that the labeled 00:13:42,400 --> 00:13:44,790 align:start position:0% a label alone and that the labeled loading here</c> 00:13:44,790 --> 00:13:44,800 align:start position:0% loading of the new extreme so down here 00:13:44,800 --> 00:13:46,980 align:start position:0% loading of the new extreme so down here this file</c> 00:13:46,980 --> 00:13:46,990 align:start position:0% this is my extremely might alert file 00:13:46,990 --> 00:13:49,230 align:start position:0% this is my extremely might alert file for as</c> 00:13:49,230 --> 00:13:49,240 align:start position:0% for my tree and I have this as 00:13:49,240 --> 00:13:50,970 align:start position:0% for my tree and I have this as parentheses node</c> 00:13:50,970 --> 00:13:50,980 align:start position:0% parentheses right here that's the node 00:13:50,980 --> 00:13:53,970 align:start position:0% parentheses right here that's the node for do</c> 00:13:53,970 --> 00:13:53,980 align:start position:0% for Homo sapiens and gorillas what I do 00:13:53,980 --> 00:13:56,430 align:start position:0% for Homo sapiens and gorillas what I do is there</c> 00:13:56,430 --> 00:13:56,440 align:start position:0% is I put a label text label right there 00:13:56,440 --> 00:13:58,500 align:start position:0% is I put a label text label right there on split</c> 00:13:58,500 --> 00:13:58,510 align:start position:0% on I'm calling a human gorilla split 00:13:58,510 --> 00:14:01,620 align:start position:0% on I'm calling a human gorilla split I've add</c> 00:14:01,620 --> 00:14:01,630 align:start position:0% I've been in my calibrations file I add 00:14:01,630 --> 00:14:04,050 align:start position:0% I've been in my calibrations file I add a name</c> 00:14:04,050 --> 00:14:04,060 align:start position:0% a line I say exclamation point node name 00:14:04,060 --> 00:14:07,170 align:start position:0% a line I say exclamation point node name equals that</c> 00:14:07,170 --> 00:14:07,180 align:start position:0% equals human gorilla splitter and that 00:14:07,180 --> 00:14:09,570 align:start position:0% equals human gorilla splitter and that that now</c> 00:14:09,570 --> 00:14:09,580 align:start position:0% that connects with this note here now 00:14:09,580 --> 00:14:11,040 align:start position:0% that connects with this note here now that maximum</c> 00:14:11,040 --> 00:14:11,050 align:start position:0% that I get my minimum the maximum 00:14:11,050 --> 00:14:15,570 align:start position:0% that I get my minimum the maximum divergence to</c> 00:14:15,570 --> 00:14:15,580 align:start position:0% divergence time okay so now I need to 00:14:15,580 --> 00:14:17,519 align:start position:0% divergence time okay so now I need to generate run</c> 00:14:17,519 --> 00:14:17,529 align:start position:0% generate a command line straining to run 00:14:17,529 --> 00:14:21,600 align:start position:0% generate a command line straining to run a we're</c> 00:14:21,600 --> 00:14:21,610 align:start position:0% a mega cc so the first thing is we're 00:14:21,610 --> 00:14:23,340 align:start position:0% a mega cc so the first thing is we're going it's</c> 00:14:23,340 --> 00:14:23,350 align:start position:0% going to use to make a cc command it's 00:14:23,350 --> 00:14:27,360 align:start position:0% going to use to make a cc command it's always the</c> 00:14:27,360 --> 00:14:27,370 align:start position:0% always just mega cc lower case and the 00:14:27,370 --> 00:14:30,090 align:start position:0% always just mega cc lower case and the first is</c> 00:14:30,090 --> 00:14:30,100 align:start position:0% first file that I'm going to specify is 00:14:30,100 --> 00:14:32,730 align:start position:0% first file that I'm going to specify is my was</c> 00:14:32,730 --> 00:14:32,740 align:start position:0% my mega analysis options file that was 00:14:32,740 --> 00:14:36,180 align:start position:0% my mega analysis options file that was the the</c> 00:14:36,180 --> 00:14:36,190 align:start position:0% the file we saved real time and uses the 00:14:36,190 --> 00:14:42,980 align:start position:0% the file we saved real time and uses the - I</c> 00:14:42,980 --> 00:14:42,990 align:start position:0% - a parameter my sequence alignment I 00:14:42,990 --> 00:14:47,670 align:start position:0% - a parameter my sequence alignment I specified tree</c> 00:14:47,670 --> 00:14:47,680 align:start position:0% specified using finish D my input tree 00:14:47,680 --> 00:14:51,600 align:start position:0% specified using finish D my input tree I I</c> 00:14:51,600 --> 00:14:51,610 align:start position:0% I used - T and that output file that I 00:14:51,610 --> 00:14:54,780 align:start position:0% I used - T and that output file that I created and</c> 00:14:54,780 --> 00:14:54,790 align:start position:0% created I specified that using - G and 00:14:54,790 --> 00:14:56,910 align:start position:0% created I specified that using - G and that I</c> 00:14:56,910 --> 00:14:56,920 align:start position:0% that calibrations file I created I 00:14:56,920 --> 00:15:02,130 align:start position:0% that calibrations file I created I specified I'm</c> 00:15:02,130 --> 00:15:02,140 align:start position:0% specified using - C and then also I'm 00:15:02,140 --> 00:15:04,890 align:start position:0% specified using - C and then also I'm going I</c> 00:15:04,890 --> 00:15:04,900 align:start position:0% going to specify the output file name I 00:15:04,900 --> 00:15:07,890 align:start position:0% going to specify the output file name I want calling</c> 00:15:07,890 --> 00:15:07,900 align:start position:0% want to use use of - oh and I'm calling 00:15:07,900 --> 00:15:10,769 align:start position:0% want to use use of - oh and I'm calling it knows</c> 00:15:10,769 --> 00:15:10,779 align:start position:0% it apes time tree and she knows 00:15:10,779 --> 00:15:13,019 align:start position:0% it apes time tree and she knows everything so</c> 00:15:13,019 --> 00:15:13,029 align:start position:0% everything here is a file name and so 00:15:13,029 --> 00:15:14,940 align:start position:0% everything here is a file name and so that's as</c> 00:15:14,940 --> 00:15:14,950 align:start position:0% that's that's what mega CC accepts as 00:15:14,950 --> 00:15:16,800 align:start position:0% that's that's what mega CC accepts as input getting</c> 00:15:16,800 --> 00:15:16,810 align:start position:0% input parameters so we're not getting 00:15:16,810 --> 00:15:20,100 align:start position:0% input parameters so we're not getting any and</c> 00:15:20,100 --> 00:15:20,110 align:start position:0% any kind of analysis settings at all and 00:15:20,110 --> 00:15:22,199 align:start position:0% any kind of analysis settings at all and so this</c> 00:15:22,199 --> 00:15:22,209 align:start position:0% so what I'm using all that I treat this 00:15:22,209 --> 00:15:25,720 align:start position:0% so what I'm using all that I treat this huge affinity</c> 00:15:25,720 --> 00:15:25,730 align:start position:0% huge ego long command large affinity 00:15:25,730 --> 00:15:27,130 align:start position:0% huge ego long command large affinity it were</c> 00:15:27,130 --> 00:15:27,140 align:start position:0% it actually be a lot longer if they were 00:15:27,140 --> 00:15:29,230 align:start position:0% it actually be a lot longer if they were asking analysis</c> 00:15:29,230 --> 00:15:29,240 align:start position:0% asking users to provide the analysis 00:15:29,240 --> 00:15:32,590 align:start position:0% asking users to provide the analysis setting using</c> 00:15:32,590 --> 00:15:32,600 align:start position:0% setting so in command okay but using 00:15:32,600 --> 00:15:34,810 align:start position:0% setting so in command okay but using that cc</c> 00:15:34,810 --> 00:15:34,820 align:start position:0% that string I go ahead I launch mega cc 00:15:34,820 --> 00:15:36,430 align:start position:0% that string I go ahead I launch mega cc so you</c> 00:15:36,430 --> 00:15:36,440 align:start position:0% so I've launched another command Mon you 00:15:36,440 --> 00:15:39,970 align:start position:0% so I've launched another command Mon you can programs</c> 00:15:39,970 --> 00:15:39,980 align:start position:0% can run it from a script other programs 00:15:39,980 --> 00:15:42,670 align:start position:0% can run it from a script other programs but all</c> 00:15:42,670 --> 00:15:42,680 align:start position:0% but mega CC runs it's going to send all 00:15:42,680 --> 00:15:44,680 align:start position:0% but mega CC runs it's going to send all feedback to</c> 00:15:44,680 --> 00:15:44,690 align:start position:0% feedback to scan it out which is easy to 00:15:44,690 --> 00:15:48,250 align:start position:0% feedback to scan it out which is easy to capture is</c> 00:15:48,250 --> 00:15:48,260 align:start position:0% capture and then the analysis done is 00:15:48,260 --> 00:15:50,430 align:start position:0% capture and then the analysis done is kind files</c> 00:15:50,430 --> 00:15:50,440 align:start position:0% kind of produce multiple results files 00:15:50,440 --> 00:15:53,950 align:start position:0% kind of produce multiple results files so the</c> 00:15:53,950 --> 00:15:53,960 align:start position:0% so a couple of notes about the the 00:15:53,960 --> 00:15:56,020 align:start position:0% so a couple of notes about the the ocular never</c> 00:15:56,020 --> 00:15:56,030 align:start position:0% ocular files so mega CC will never 00:15:56,030 --> 00:15:59,800 align:start position:0% ocular files so mega CC will never overwrite a</c> 00:15:59,800 --> 00:15:59,810 align:start position:0% overwrite any files if it encounters a 00:15:59,810 --> 00:16:02,890 align:start position:0% overwrite any files if it encounters a naming find</c> 00:16:02,890 --> 00:16:02,900 align:start position:0% naming collision mega CC will just find 00:16:02,900 --> 00:16:05,020 align:start position:0% naming collision mega CC will just find a American</c> 00:16:05,020 --> 00:16:05,030 align:start position:0% a numeric value that uniquely American 00:16:05,030 --> 00:16:07,930 align:start position:0% a numeric value that uniquely American to a</c> 00:16:07,930 --> 00:16:07,940 align:start position:0% to append to the name and there are a 00:16:07,940 --> 00:16:09,340 align:start position:0% to append to the name and there are a couple are</c> 00:16:09,340 --> 00:16:09,350 align:start position:0% couple of Manian conventions that are 00:16:09,350 --> 00:16:12,790 align:start position:0% couple of Manian conventions that are used Oh</c> 00:16:12,790 --> 00:16:12,800 align:start position:0% used for the files so is that - Oh 00:16:12,800 --> 00:16:16,720 align:start position:0% used for the files so is that - Oh parameter was</c> 00:16:16,720 --> 00:16:16,730 align:start position:0% parameter is used the value that was 00:16:16,730 --> 00:16:19,320 align:start position:0% parameter is used the value that was given names</c> 00:16:19,320 --> 00:16:19,330 align:start position:0% given will prefix all the file names 00:16:19,330 --> 00:16:22,090 align:start position:0% given will prefix all the file names otherwise name</c> 00:16:22,090 --> 00:16:22,100 align:start position:0% otherwise the input data file name 00:16:22,100 --> 00:16:24,670 align:start position:0% otherwise the input data file name that's again</c> 00:16:24,670 --> 00:16:24,680 align:start position:0% that's used will prefix all the again 00:16:24,680 --> 00:16:27,400 align:start position:0% that's used will prefix all the again results that</c> 00:16:27,400 --> 00:16:27,410 align:start position:0% results finally and so for that 00:16:27,410 --> 00:16:29,770 align:start position:0% results finally and so for that real-time done</c> 00:16:29,770 --> 00:16:29,780 align:start position:0% real-time analysis once it's done 00:16:29,780 --> 00:16:34,150 align:start position:0% real-time analysis once it's done running go</c> 00:16:34,150 --> 00:16:34,160 align:start position:0% running it produced five files let's go 00:16:34,160 --> 00:16:36,580 align:start position:0% running it produced five files let's go to relative</c> 00:16:36,580 --> 00:16:36,590 align:start position:0% to Newark clouds there it was a relative 00:16:36,590 --> 00:16:38,320 align:start position:0% to Newark clouds there it was a relative and were</c> 00:16:38,320 --> 00:16:38,330 align:start position:0% and exact divergence times that were 00:16:38,330 --> 00:16:40,900 align:start position:0% and exact divergence times that were calculated read</c> 00:16:40,900 --> 00:16:40,910 align:start position:0% calculated so everybody I think it read 00:16:40,910 --> 00:16:42,130 align:start position:0% calculated so everybody I think it read knows other</c> 00:16:42,130 --> 00:16:42,140 align:start position:0% knows it would format with these other 00:16:42,140 --> 00:16:45,640 align:start position:0% knows it would format with these other three big</c> 00:16:45,640 --> 00:16:45,650 align:start position:0% three formats there there there big 00:16:45,650 --> 00:16:47,050 align:start position:0% three formats there there there big difference in</c> 00:16:47,050 --> 00:16:47,060 align:start position:0% difference I want to go over what's in 00:16:47,060 --> 00:16:51,580 align:start position:0% difference I want to go over what's in them txt</c> 00:16:51,580 --> 00:16:51,590 align:start position:0% them so the Apes country file dot txt 00:16:51,590 --> 00:16:54,700 align:start position:0% them so the Apes country file dot txt that's by</c> 00:16:54,700 --> 00:16:54,710 align:start position:0% that's the main output is produced by 00:16:54,710 --> 00:16:57,460 align:start position:0% that's the main output is produced by real tabular</c> 00:16:57,460 --> 00:16:57,470 align:start position:0% real time and so this is a yeah tabular 00:16:57,470 --> 00:16:59,680 align:start position:0% real time and so this is a yeah tabular output were</c> 00:16:59,680 --> 00:16:59,690 align:start position:0% output appears all the values that were 00:16:59,690 --> 00:17:02,470 align:start position:0% output appears all the values that were calculated and</c> 00:17:02,470 --> 00:17:02,480 align:start position:0% calculated by the real time analysis and 00:17:02,480 --> 00:17:06,280 align:start position:0% calculated by the real time analysis and so names</c> 00:17:06,280 --> 00:17:06,290 align:start position:0% so we have all of our our sequence names 00:17:06,290 --> 00:17:08,470 align:start position:0% so we have all of our our sequence names here everything</c> 00:17:08,470 --> 00:17:08,480 align:start position:0% here and we have a map theory everything 00:17:08,480 --> 00:17:10,210 align:start position:0% here and we have a map theory everything in a</c> 00:17:10,210 --> 00:17:10,220 align:start position:0% in the tree gets a node ID and we have a 00:17:10,220 --> 00:17:13,390 align:start position:0% in the tree gets a node ID and we have a mapping our</c> 00:17:13,390 --> 00:17:13,400 align:start position:0% mapping for all the load IDs we have our 00:17:13,400 --> 00:17:15,580 align:start position:0% mapping for all the load IDs we have our calculated errors</c> 00:17:15,580 --> 00:17:15,590 align:start position:0% calculated run times standard errors 00:17:15,590 --> 00:17:18,550 align:start position:0% calculated run times standard errors evolutionary exact</c> 00:17:18,550 --> 00:17:18,560 align:start position:0% evolutionary grades there are exact 00:17:18,560 --> 00:17:20,650 align:start position:0% evolutionary grades there are exact divergence time</c> 00:17:20,650 --> 00:17:20,660 align:start position:0% divergence times here then real time 00:17:20,660 --> 00:17:24,160 align:start position:0% divergence times here then real time also upper</c> 00:17:24,160 --> 00:17:24,170 align:start position:0% also calculates lower and upper 00:17:24,170 --> 00:17:29,500 align:start position:0% also calculates lower and upper confidence the</c> 00:17:29,500 --> 00:17:29,510 align:start position:0% confidence intervals all the 00:17:29,510 --> 00:17:31,900 align:start position:0% confidence intervals all the calculations this</c> 00:17:31,900 --> 00:17:31,910 align:start position:0% calculations produce a summary file this 00:17:31,910 --> 00:17:35,080 align:start position:0% calculations produce a summary file this example txt</c> 00:17:35,080 --> 00:17:35,090 align:start position:0% example it's H time tree summary dot txt 00:17:35,090 --> 00:17:37,990 align:start position:0% example it's H time tree summary dot txt and is</c> 00:17:37,990 --> 00:17:38,000 align:start position:0% and so what we've done with this is 00:17:38,000 --> 00:17:39,370 align:start position:0% and so what we've done with this is we've in</c> 00:17:39,370 --> 00:17:39,380 align:start position:0% we've written it in 00:17:39,380 --> 00:17:43,000 align:start position:0% we've written it in follow we</c> 00:17:43,000 --> 00:17:43,010 align:start position:0% follow four men and do that because we 00:17:43,010 --> 00:17:44,860 align:start position:0% follow four men and do that because we want pretty</c> 00:17:44,860 --> 00:17:44,870 align:start position:0% want it to be easy at first it's pretty 00:17:44,870 --> 00:17:46,840 align:start position:0% want it to be easy at first it's pretty much and</c> 00:17:46,840 --> 00:17:46,850 align:start position:0% much any programming language and 00:17:46,850 --> 00:17:48,160 align:start position:0% much any programming language and scripting a</c> 00:17:48,160 --> 00:17:48,170 align:start position:0% scripting language already has a 00:17:48,170 --> 00:17:50,370 align:start position:0% scripting language already has a ready-made format</c> 00:17:50,370 --> 00:17:50,380 align:start position:0% ready-made parser for this file format 00:17:50,380 --> 00:17:53,890 align:start position:0% ready-made parser for this file format and not</c> 00:17:53,890 --> 00:17:53,900 align:start position:0% and so here we put all our not 00:17:53,900 --> 00:17:56,020 align:start position:0% and so here we put all our not calculated that</c> 00:17:56,020 --> 00:17:56,030 align:start position:0% calculated analysis statistics that 00:17:56,030 --> 00:17:57,520 align:start position:0% calculated analysis statistics that don't output</c> 00:17:57,520 --> 00:17:57,530 align:start position:0% don't belong even need the other output 00:17:57,530 --> 00:18:00,340 align:start position:0% don't belong even need the other output files also</c> 00:18:00,340 --> 00:18:00,350 align:start position:0% files any warnings or errors would also 00:18:00,350 --> 00:18:04,450 align:start position:0% files any warnings or errors would also be there</c> 00:18:04,450 --> 00:18:04,460 align:start position:0% be logged at this file okay now there 00:18:04,460 --> 00:18:07,300 align:start position:0% be logged at this file okay now there was and</c> 00:18:07,300 --> 00:18:07,310 align:start position:0% was another file that was produced and 00:18:07,310 --> 00:18:08,920 align:start position:0% was another file that was produced and it's it's</c> 00:18:08,920 --> 00:18:08,930 align:start position:0% it's really an extra two file it's 00:18:08,930 --> 00:18:10,450 align:start position:0% it's really an extra two file it's called tree</c> 00:18:10,450 --> 00:18:10,460 align:start position:0% called Apes underscore time tree 00:18:10,460 --> 00:18:13,600 align:start position:0% called Apes underscore time tree underscore we've</c> 00:18:13,600 --> 00:18:13,610 align:start position:0% underscore Nexus duck TR e and we've 00:18:13,610 --> 00:18:16,000 align:start position:0% underscore Nexus duck TR e and we've kind to</c> 00:18:16,000 --> 00:18:16,010 align:start position:0% kind of we custom formatted this file to 00:18:16,010 --> 00:18:17,770 align:start position:0% kind of we custom formatted this file to work viewer</c> 00:18:17,770 --> 00:18:17,780 align:start position:0% work with the fig tree tree viewer 00:18:17,780 --> 00:18:21,640 align:start position:0% work with the fig tree tree viewer application this</c> 00:18:21,640 --> 00:18:21,650 align:start position:0% application and what's nice about this 00:18:21,650 --> 00:18:23,650 align:start position:0% application and what's nice about this is fig</c> 00:18:23,650 --> 00:18:23,660 align:start position:0% is that you can open up that file a fig 00:18:23,660 --> 00:18:25,180 align:start position:0% is that you can open up that file a fig tree keep</c> 00:18:25,180 --> 00:18:25,190 align:start position:0% tree there's a lot of things that keep 00:18:25,190 --> 00:18:27,820 align:start position:0% tree there's a lot of things that keep tree of</c> 00:18:27,820 --> 00:18:27,830 align:start position:0% tree can do to customize the display of 00:18:27,830 --> 00:18:30,130 align:start position:0% tree can do to customize the display of the are</c> 00:18:30,130 --> 00:18:30,140 align:start position:0% the results you see these branches are 00:18:30,140 --> 00:18:31,960 align:start position:0% the results you see these branches are colored have</c> 00:18:31,960 --> 00:18:31,970 align:start position:0% colored here and in my example I have 00:18:31,970 --> 00:18:33,610 align:start position:0% colored here and in my example I have that calculated</c> 00:18:33,610 --> 00:18:33,620 align:start position:0% that color based on the calculated 00:18:33,620 --> 00:18:36,550 align:start position:0% that color based on the calculated evolutionary tree</c> 00:18:36,550 --> 00:18:36,560 align:start position:0% evolutionary rate and also the new tree 00:18:36,560 --> 00:18:38,110 align:start position:0% evolutionary rate and also the new tree can type</c> 00:18:38,110 --> 00:18:38,120 align:start position:0% can do things like show the know type 00:18:38,120 --> 00:18:40,960 align:start position:0% can do things like show the know type error like</c> 00:18:40,960 --> 00:18:40,970 align:start position:0% error bars and you can do a model like 00:18:40,970 --> 00:18:42,720 align:start position:0% error bars and you can do a model like interesting visualize</c> 00:18:42,720 --> 00:18:42,730 align:start position:0% interesting things to help you visualize 00:18:42,730 --> 00:18:45,730 align:start position:0% interesting things to help you visualize some of</c> 00:18:45,730 --> 00:18:45,740 align:start position:0% some of the calculated values and of 00:18:45,740 --> 00:18:49,060 align:start position:0% some of the calculated values and of course resulting</c> 00:18:49,060 --> 00:18:49,070 align:start position:0% course you compute this the resulting 00:18:49,070 --> 00:18:51,370 align:start position:0% course you compute this the resulting negative we</c> 00:18:51,370 --> 00:18:51,380 align:start position:0% negative treat viewers whatever but we 00:18:51,380 --> 00:18:52,870 align:start position:0% negative treat viewers whatever but we don't that</c> 00:18:52,870 --> 00:18:52,880 align:start position:0% don't there's a few extra features that 00:18:52,880 --> 00:18:54,850 align:start position:0% don't there's a few extra features that you coloring</c> 00:18:54,850 --> 00:18:54,860 align:start position:0% you have a fig tree like this coloring 00:18:54,860 --> 00:19:00,180 align:start position:0% you have a fig tree like this coloring of up</c> 00:19:00,180 --> 00:19:00,190 align:start position:0% of the the branches okay so wrapping up 00:19:00,190 --> 00:19:02,530 align:start position:0% of the the branches okay so wrapping up so the</c> 00:19:02,530 --> 00:19:02,540 align:start position:0% so we've talked about what is the 00:19:02,540 --> 00:19:04,360 align:start position:0% so we've talked about what is the computational the</c> 00:19:04,360 --> 00:19:04,370 align:start position:0% computational cord omega so that's the 00:19:04,370 --> 00:19:07,210 align:start position:0% computational cord omega so that's the calculation computes</c> 00:19:07,210 --> 00:19:07,220 align:start position:0% calculation engine that computes 00:19:07,220 --> 00:19:10,390 align:start position:0% calculation engine that computes everything a</c> 00:19:10,390 --> 00:19:10,400 align:start position:0% everything in mega so it has a 00:19:10,400 --> 00:19:11,920 align:start position:0% everything in mega so it has a command-line is</c> 00:19:11,920 --> 00:19:11,930 align:start position:0% command-line interface which is 00:19:11,930 --> 00:19:15,100 align:start position:0% command-line interface which is optimized in</c> 00:19:15,100 --> 00:19:15,110 align:start position:0% optimized for automation working in 00:19:15,110 --> 00:19:17,920 align:start position:0% optimized for automation working in analysis mega</c> 00:19:17,920 --> 00:19:17,930 align:start position:0% analysis pipelines whenever you run mega 00:19:17,930 --> 00:19:20,770 align:start position:0% analysis pipelines whenever you run mega cc mega</c> 00:19:20,770 --> 00:19:20,780 align:start position:0% cc you always have to provide this mega 00:19:20,780 --> 00:19:24,100 align:start position:0% cc you always have to provide this mega analysis to</c> 00:19:24,100 --> 00:19:24,110 align:start position:0% analysis options file this file needs to 00:19:24,110 --> 00:19:25,660 align:start position:0% analysis options file this file needs to be user</c> 00:19:25,660 --> 00:19:25,670 align:start position:0% be generated using the graphical user 00:19:25,670 --> 00:19:28,270 align:start position:0% be generated using the graphical user detect an</c> 00:19:28,270 --> 00:19:28,280 align:start position:0% detect things and we also went to an 00:19:28,280 --> 00:19:29,860 align:start position:0% detect things and we also went to an example treaty</c> 00:19:29,860 --> 00:19:29,870 align:start position:0% example of how to create a time treaty 00:19:29,870 --> 00:19:35,860 align:start position:0% example of how to create a time treaty in xcc</c> 00:19:35,860 --> 00:19:35,870 align:start position:0% in mega xcc okay so mega xcc 00:19:35,870 --> 00:19:43,050 align:start position:0% in mega xcc okay so mega xcc is website</c> 00:19:43,050 --> 00:19:43,060 align:start position:0% 00:19:43,060 --> 00:19:48,790 align:start position:0% www.levitt.com been</c> 00:19:48,790 --> 00:19:48,800 align:start position:0% www.levitt.com a sees not yet been 00:19:48,800 --> 00:19:51,220 align:start position:0% www.levitt.com a sees not yet been released soon</c> 00:19:51,220 --> 00:19:51,230 align:start position:0% released for for mac OS it's coming soon 00:19:51,230 --> 00:19:53,260 align:start position:0% released for for mac OS it's coming soon but mega</c> 00:19:53,260 --> 00:19:53,270 align:start position:0% but there still is mega 00:19:53,270 --> 00:19:55,450 align:start position:0% but there still is mega ncc that</c> 00:19:55,450 --> 00:19:55,460 align:start position:0% ncc which is available to run on that 00:19:55,460 --> 00:19:57,220 align:start position:0% ncc which is available to run on that illness 10.9</c> 00:19:57,220 --> 00:19:57,230 align:start position:0% illness networks with mavericks 10.9 00:19:57,230 --> 00:19:59,980 align:start position:0% illness networks with mavericks 10.9 plus