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

Search NCBI. For options run phyutility -h ncbisearch.

parse

Parse genbank results. For options run phyutility -h parse.