weighted partial super bootstrap
Union concatenate alignments according to inputting order into a Super-MSA with PHYLIP format.
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
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
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
https://wpsboot.page.link/main
- 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