Multiple Sequence Alignment

The commande msa compute multiple sequence alignment of any partition of the pangenome. The command uses mafft with default options to perform the alignment. Using multiple cpus with the --cpu argument is recommended as multiple alignment can be quite demanding in computational resources.

This command can be used as follow:

ppanggolin msa -p pangenome.h5

By default it will write the strict ‘core’ (genes that are present in absolutely all genomes) and remove any duplicated genes. Beware however that, if you have many genomes (over 1000), the core will likely be either very small or even empty if you have fragmented genomes.

It will write one MSA for each family. You can then provide the directory where the MSA are written to IQ-TREE for example, to do phylogenetic analysis.

Modify the partition with --partition

You can change the partition which is written, by using the –partition option.

for example will compute MSA for all the persistent gene families.

ppanggolin msa -p pangenome.h5 --partition persistent

Supported partitions are core, persistent, shell, cloud, softcore, accessory. If you need specific filters, you can submit a request in the issue tracker with your requirements. You can also directly implement the new filter and submit a Pull Request (instructions for contribution can be found here). Most filters should be quite straightforward to add.

Chose to align dna or protein sequences with --source

You can specify whether to use dna or protein sequences for the MSA by using --source. It uses protein sequences by default.

ppanggolin msa -p pangenome.h5 --source dna

Write a single whole MSA file with --phylo

It is also possible to write a single whole genome MSA file, which many phylogenetic software accept as input, by using the --phylo option as such:

ppanggolin msa -p pangenome.h5 --phylo

This will concatenate all of the family MSA into a single MSA, with one sequence for each genome.