HMMPhylo

HMMPhylo is a library/docker container for taking the results of HMMsearch and creating phylogenetic trees from them. This is used to study PPK protein sequences in Eukaryotes and other kingdoms.

Tools Used

• Delbian (Standard Linux Image)
• Python is used to webscrape all the uniprot IDs used in the results of the HMMsearch
• MAFFT (MSA)
• TrimAL
• IQ-TREE

Local Machine

Prerequisites

Before you continue, ensure you have met the following requirements:

• You have installed Docker for your operating system.
• If you are on windows then you will also need WSL.
• Setting up the System

git clone https://github.com/keith-harrison/hmmphylo/
cd hmmphylo
docker-compose up -d
docker-compose run --rm hmmphylo
dos2unix initialtree.sh
dos2unix prunetree.sh

• Running initialtree.sh (Gives phylogeny of the sequences given from two given PFAM alignments/HMMsearch results)

./initialtree.sh

• Running prunetree.sh (Gives refined phylogeny of pruned tree using manual pruned file from ITOL)

#NAME THE FILE pruneddraft.nwk and provide the concatenated_ready_seq.fa file
./prunetree.sh

Contributing

Pull requests are welcome. For major changes, please open an issue first to discuss what you would like to change.

Please make sure to update tests as appropriate.

Do More Research on :

cut_ga (gathering threshold) gappy out