phyutility(1)
tools for manipulating sequences and phylogenies
SYNOPSIS
phyutility
<command> <options>
DESCRIPTION
Phyutility is a command line program that performs simple analyses or modifications on both trees and data matrices.
OPTIONS
To get help on a specific command use option -h <command>
COMMANDS
for trees:
- consensus
-
Calculate consensus trees. Use like -con -t <threshold> -in <infile> -out <outfile>.
- convert
-
Convert tree files. Use like -vert -in <infile> -out <outfile>.
- leafstab
-
Leaf stability index calculation. Use like -ls -in <infile>.
- linmove
-
Lineage movement calculation. Use like -lm -names <tip names> -tree <consensus> -in <infile> -out <outfile>.
- prune
-
Prune lineages. Use like -pr -names <tip names> -in <infile> -out <outfile>.
- reroot
-
Reroot trees. Use like -rr -names <tip names> -in <infile> -out <outfile>.
- thin
-
Thin trees. Use like -tt # -in <infile> -out <outfile>.
- treesupp
-
Support for a set of trees. Use like -ts -tree <tree> -in <infile> -out <outfile>.
- for seqs:
-
- clean
-
Trim seqs based on threshold. Use like -clean # -in <infile> -out <outfile> -aa <to force aa>.
- concat
-
Concatenate alignments. Use like -concat -in <infiles> -out <outfile> -aa <to force aa>.
- ncbiget
-
Fetch seqs from NCBI. For options run phyutility -h ncbiget.
- ncbisearch
-
Seach NCBI. For options run phyutility -h ncbisearch.
- parse
-
Parse genbank results. For options run phyutility -h parse.
EXAMPLE
- phyutility -con -t 0.5 -in testall.tre -out test.con
-
Consensus the set of trees in testall.tre collapsing branches with less than 0.5 frequency.
- phyutility -vert -in test.tre -out testvert.nex
-
Convert the tree file from newick in test.tre into nexus in testvert.nex.
- phyutility -concat -in test.aln test2.aln -out testall.nex
-
Concatenate 2 alignment files into nexus in testall.nex.
