YuuMJ1997/EukPhylo
1
0
Fork 0
mirror of http://43.156.76.180:8026/YuuMJ/EukPhylo.git synced 2025-12-27 05:10:28 +08:00
Code Issues Packages Projects Releases Wiki Activity

Updated Home (markdown)

Godwin Ani 2024-08-12 10:30:56 -04:00
parent 7cf4067948
commit e84da77f3e
1 changed files with 1 additions and 1 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
Home.md

@ -1,4 +1,4 @@
PhyloToL version 6 is designed to be a modular, accessible pipeline that includes sophisticated data curation methods, including a newly designed method of phylogeny-informed contamination removal, gene families homology estimation, and generation multisequence alignments (MSAs) and gene trees.
PhyloToL version 6 is designed to be a modular, accessible pipeline that includes sophisticated data curation methods, including a newly designed method of phylogeny-informed contamination removal, gene families homology estimation, and generating multisequence alignments (MSAs) and gene trees.
The core PhyloToL pipeline comprises two main components, which we refer to as PhyloToL parts 1 and 2. PhyloToL part 1 takes input sequences from a whole genome or transcriptome assembly, applies several curation steps, and provides initial homology assessment against a customizable database of reference sequences to assign GFs. Part one outputs a fasta file of curated nucleotide and amino acid sequences with gene families assigned, as well as a dataset of descriptive statistics (e.g. length, coverage, and composition) for each input sample. PhyloToL part 2 is highly modular; for a given selection of taxa and GFs it stringently assesses homology by iterating the tool Guidance (Penn et al., 2010; Sela et al., 2015), which outputs an MSA for each gene family. From MSAs it builds gene trees, and then includes an innovative workflow for tree topology-based contamination removal.