Bali-Phy3

BAli_Phy V 3.6.1

BAli-Phy is software by Ben Redelings that estimates multiple sequence alignments and evolutionary trees from DNA, amino acid, or codon sequences. It uses likelihood-based evolutionary models of substitutions and insertions and deletions to place gaps. It has been used in published analyses on data sets up to 117 taxa.

BAli-Phy can be run in parallel by making several individual runs simultaneously on a single core, and combining the results. A new CIPRES interface supports this capability for up to 6 runs. Please see the BAli-Phy manual for more information.

Worked examples are here.

Restarting: Bali-Phy does not run checkpointing at this time. While it is posisble to restart implementations in Docker, our security policies do not allow us to support that option. If you do a CIPRES "restart" on a Bali-Phy run without changing the command line in any way, the application will repeat the analysis with a new set of results, rather than continue the existing run. However, the CIPRES restart feature allows us to support the use of the consensus tree feature. The restart feature was implemented to make this possible. When a run completes, one can edit the run parameters to request consensus trees calculations on data created in the previous run.

Input files: In CIPRES implementation, BAli-Phy accepts as input up to 6 files (genes/partitions) in fasta format. One can also provide a config file, instead of using the interface. Also, one can provide a starting tree file in Newick format.

Output files:

The table below shows the kinds of results returned by CIPRES Science Gateway:

Input File Names Sample File from a Test
input file 5d.fasta
   
Sample Output File Type File Name
log file yourjob.log
tree file(s) yourjob.trees
operators file mcmc.operators
   
   

If you use BAli-Phy here, please cite:
Redelings, B. D. (2021) BAli-Phy version 3: model-based co-estimation of alignment and phylogeny. Bioinformatics 37, 3032-3034 10.1093/bioinformatics/btab129

 

If there is a tool or a feature you need, please let us know.

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