wpSBOOT

weighted partial super bootstrap

src/concatenate.pl

Union concatenate alignments according to inputting order into a Super-MSA with PHYLIP format.

requirement

Please install the following modules from BioPerl. Detailed information in BioPerl.

• Bio::AlignIO
• Bio::Align::Utilities
• Bio::LocatableSeq

>perl -MCPAN -e shell
cpan> install Bio::AlignIO

usage

concatenate.pl [options] --aln alignment1 alignment2 ... (at least two alignments) --out result
	--intersect: only concatenate sequences appearing in all alignments, otherwise missing sequence is replaced with gap (default)
	--random: concatenate order is random
	--size N: only concatenate first N alignments from inputting, exclusive with replicate mode
	--replicate NUM: replicate one alignment in NUM times, exclusive with size mode

an example commend

perl concatenate.pl --aln MAFFT.fasta Muscle.fasta ClustalW.fasta T-Coffee.fasta --out superMSA.phylip

corresponding running log

How to concatenate:
	size: 4 alignments
	alignments:
		MAFFT.fasta
		Muscle.fasta
		ClustalW.fasta
		T-Coffee.fasta
	output: superMSA.phylip

web server

https://wpsboot.page.link/main

reference

• original paper: J.-M. Chang, E. W. Floden, J. Herrero, O. Gascuel, P. Di Tommaso, and C. Notredame, Incorporating alignment uncertainty into Felsenstein’s phylogenetic bootstrap to improve its reliability. Bioinformatics, Feb. 2019
• related work: H Ashkenazy, I Sela, E Levy Karin, G Landan, T Pupko, Multiple sequence alignment averaging improves phylogeny reconstruction. Systematic biology, 2019 68 (1), 117-130