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Arkadiy-Garber / ParaHunter

Identification of gene paralogs in genomes, and calculation of dS and dN/dS values for paralogous gene pairs
GNU General Public License v3.0
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codeml duplicates gene-paralogs paml paralogs

readme

ParaHunter

If you found this software useful to your research please cite as follows:

Garber, AI and Miller, SR (2020) ParaHunter: identification of gene paralogs in genomes. GitHub repository: https://github.com/Arkadiy-Garber/ParaHunter.

ParaHunter uses MMseqs2 to cluster sequences from a single genomic dataset, based on a set of user-defined parameters. The clustered genes are then aligned using Muscle and PAL2NAL, and pairwise dS, dN, and dN/dS values are calculated using PAML.

easy-installation:

git clone https://github.com/Arkadiy-Garber/ParaHunter.git
cd ParaHunter
bash setup.sh
source activate parahunt

quick-start

ParaHunter.sh -a genomeOrfs_aa.faa -n genomeOrfs_nuc.ffn

setting minimum amino acid identity for clustering to 35%, with query coverage of at least 50%

ParaHunter.sh -a genomeOrfs_aa.faa -n genomeOrfs_nuc.ffn -m 0.35 -c 0.5

Tutorial (Binder)

This software uses PAML, in addition to other tools like MMseqs2 and Muscle. If you would like to learn more about what is going on under the hood of this program, and some of the theoretical framework behind the evolutionary biology of gene divergence estimates, please see the following slideshow and associated video:

Slideshow | Video presentation

Walkthrough

If you'd like to try out this program in a virtual terminal session with all dependencies and test dataset pre-loaded, hit the 'launch binder' button below, and follow the commands in 'Walkthrough'

Binder

(Initially forked from here. Thank you to the awesome binder team!)

You can also follow along in this linked video: Video presentation

These videos were made as part of the Bioinformatics Virtual Coordination Network :)

Using PAML

Enter the first direcotry

cd interspecies_example//

Align the FASTA amino acid file

muscle -in MNBX01000583.1_4.faa -out MNBX01000583.1_4.fa

Make a codon alignment from the peptide alignment and nucleotide sequence

pal2nal.pl MNBX01000583.1_4.fa MNBX01000583.1_4.ffn -output fasta > MNBX01000583.1_4.codonalign.fa

Check that the correct input/output files are in the codeml.ctl file

less codeml.ctl

Run codeml

codeml codeml.ctl

Enter the second directory

cd intraspecies_example/

Align the FASTA amino acid file

muscle -in NC_009928.1_232.faa -out NC_009928.1_232.fa

Make a codon alignment from the peptide alignment and nucleotide sequence

pal2nal.pl NC_009928.1_232.fa NC_009928.1_232.ffn -output fasta > NC_009928.1_232.codonalign.fa

Run codeml after checking out the input/output codeml.ctl file

codeml codeml.ctl

ParaHunter tutorial

Print the ParaHunter help menu

Parahunter.sh -h

Run program on the test dataset

cd ParaHunter/
cd cyanothece/
ParaHunter.sh -a CyanothecePCC7425.faa -n CyanothecePCC7425.ffn -l ../codeml-2.ctl