EasyCGTree: a pipeline for prokaryotic phylogenomic analysis based on core gene sets.

ABSTRACT:

Background

Genome-scale phylogenetic analysis based on core gene sets is routinely used in microbiological research. However, the techniques are still not approachable for individuals with little bioinformatics experience. Here, we present EasyCGTree, a user-friendly and cross-platform pipeline to reconstruct genome-scale maximum-likehood (ML) phylogenetic tree using supermatrix (SM) and supertree (ST) approaches.

Results

EasyCGTree was implemented in Perl programming languages and was built using a collection of published reputable programs. All the programs were precompiled as standalone executable files and contained in the EasyCGTree package. It can run after installing Perl language environment. Several profile hidden Markov models (HMMs) of core gene sets were prepared

SUBMITTER: Zhang DF 

PROVIDER: S-EPMC10576351 | biostudies-literature | 2023 Oct

REPOSITORIES: biostudies-literature