YuuMJ1997/EukPhylo
1
0
Fork 0
mirror of http://43.156.76.180:8026/YuuMJ/EukPhylo.git synced 2025-12-29 16:30:24 +08:00
Code Issues Packages Projects Releases Wiki Activity

Updated PhyloToL Part 2: MSAs, trees, and contamination loop (markdown)

Katzlab 2024-08-13 18:52:24 -04:00
parent 04ee27ef19
commit 634ac07573
1 changed files with 1 additions and 1 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
PhyloToL-Part-2:-MSAs,-trees,-and-contamination-loop.md

@ -154,7 +154,7 @@ indicates that the a sequence from the choanoflagellate Op_ch_Dgra should be rem
In clade-grabbing mode, each row again represents a rule. This time, there are five columns. The first column gives the target taxonomic group for which you are clade grabbing. Here you can give a ten-digit code, a subset of a code, or even the path to a text file containing a list of multiple codes if they don't all share a precise enough prefix. The third column gives the minimum number of target taxa that must be in a clade for it to be kept, and the second column gives the minimum proportion (or absolute number of >1) of taxa in that clade that are not in the target group. The fourth column allows you to give a list of 'special' taxa (or just a ten-digit code or a subset of a code), X of which must be present in a clade for it to be selected, where X is the number in the fifth column. For example, the line
|Sr_ci | 0.1 | 13 | ciliate_genomes.txt | 1|
|-|-|-|-|
|-|-|-|-|-|
indicates that all ciliate sequences should be removed if they don't fall in a clade with at least 13 ciliate species (unique ten digit codes beginning with Sr_ci), where no more than 1/10 of the species in the clade are non-ciliates, and containing at least 1 sequence that begins with a prefix listed in the ciliate_genomes.txt file (i.e., if you're more confident in genomic data, you may want to make sure that there's a genome in your clade).