syntenic_orthogroups: construct syntenic orthogroups from pairwise blast
In jtlovell/GENESPACE: Synteny- and orthology-constrained comparative genomics

syntenic_orthogroups

R Documentation

construct syntenic orthogroups from pairwise blast

Description

syntenic_orthogroups integrates many pairwise results from synteny into vectors of syntenic orthogroups. Also can re-run orthofinder within blocks and re-calculate orthogroups from those results.

syntenic_orthogroups combine blast hits to cluster hits into syntenic orthogroups.

run_orthofinderInBlk Loop through the pairwise combination of genomes and run orthofinderInBlk

ofInBlk_engine Main engine to run orthofinder in blocks

Usage

syntenic_orthogroups(gsParam, updateArrays)

run_orthofinderInBlk(gsParam, overwrite = FALSE)

ofInBlk_engine(gsParam, genome1, genome2, overwrite)

Arguments

`gsParam`	A list of genespace parameters created by init_genespace.
`updateArrays`	logical, should arrays be updated?
`overwrite`	logical, should results be overwritten?
`genome1`	character vector with the query genome for orthofinderInBlk
`genome2`	character vector with the target genome for orthofinderInBlk