coreGenomePhylogeny

Author: Priya Lakra

Description

This is the script for constructing core genome phylogeny for taxonomic purposes. It involves extraction of core genome from the genome assemblies of closely and/or distantly related species, and employing this core genome for construction of phylogenomic tree.

Requirements:

get_homologues

get_homologues package is required for extracting core and pan genomes among different species.

MAFFT

MAFFT is used for generating multiple sequence alignment.

Sequence matrix (optional)

For concatenating alignments into a super matrix, one can use

1. Sequence matrix
2. Custom scripts

Phylogeny tools

IQtree and MEGA X can be used for generating phylogenomic trees.

Tree visualization tools

iTOL is used for tree visualization and editing. Figtree can also be used.

Steps:

1. Clone the repository with

`git clone https://github.com/PriyaLakr/coreGenomePhylogeny.git` 
`cd PATH/TO/coreGenomePhylogeny`

2. Installing all dependencies

`bash pl_install_depend.sh`

You can check installation information in the file "install.info"

3. Extracting core genome using get_homologues

`bash pl_getcg.sh [options]`

for help: run bash pl_getcg.sh -h

4. Filtering orthologous genes

Steps:

4.1. Align genes

4.2. Select genes containing less than 5% gaps in their multiple sequence alignments

 `bash pl_treegen.sh [options]`

for help: run bash pl_treegen.sh -h

4.3. Create a super matrix using either the given script, your custom script and/or sequence matrix

`bash pl_concat.sh`

for help: run bash pl_concat.sh -h

Notes: Another way is to create trees using individual gene files and concatenate individual gene trees to create a super tree. Read first if you really require this approach.

5. Generating the phylogenomic tree

`bash pl_treegen.sh [options]`

6. Visualize and edit tree newick file in your choice of tools

Reference data adapted from Lakra, P et al., 2021.