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Not sure if you have been through biojava3-phylo module that is a wrapper
for forester phylogenomics library for constructing phylogenetic trees
found at https://code.google.com/p/forester/wiki/forester. At the time
forester was using svn and we didn't want to check-in/fork the source so we
reference the forester jar file and thus are missing any important bug
fixes. The forester java code covers just about everything you can imagine
related to phylogenetic algorithms but is primarily used as an application.
Thus the thought was to make convenience api's in BioJava to hide the
implementation details required using the forester API.
The Phylip format can refer to the MSA format, like FASTA format (see here the format explanation) or to a distance matrix format (see here the format explanation). I guess @sbliven that the discussion was about the MSA format. I have seen that forester contains methods to write the DistanceMatrix object as a Phylip format, but I could not find a parser for the MSA format.
In the documentation of their application (see Input and Output Formats section) they do not list PHYLIP as a supported format, but I tried the application and it can read phylip MSA formats, so there must be a parser in the forester package.
Since Phylip seems to be a general format for MSA storage (but less powerful than FASTA), is there a need to provide a parser in the core module of biojava, or using the forester one only for the phylo module is enough? Since we had already an implementation it would be just a design issue.
In the forester library:
Probably the GeneralMsaParser class is used to parse Phylip MSA formats (the documentation is poor).
There is also a SymmetricalDistanceMatrixParser class for symmetrical distances in Phylip format.
Activity
willishf commentedon May 12, 2014
Spencer
Not sure if you have been through biojava3-phylo module that is a wrapper
for forester phylogenomics library for constructing phylogenetic trees
found at https://code.google.com/p/forester/wiki/forester. At the time
forester was using svn and we didn't want to check-in/fork the source so we
reference the forester jar file and thus are missing any important bug
fixes. The forester java code covers just about everything you can imagine
related to phylogenetic algorithms but is primarily used as an application.
Thus the thought was to make convenience api's in BioJava to hide the
implementation details required using the forester API.
Scooter
http://biojava.org/wiki/BioJava:CookBook:Phylo:Overview
On Mon, May 12, 2014 at 6:16 AM, Spencer Bliven notifications@github.comwrote:
sbliven commentedon May 15, 2014
Ok, if forester's parsers can handle the phylip format then this should definitely be closed.
andreasprlic commentedon Jun 27, 2014
just for reference, we used to have support for Phylip in Biojava 1 https://github.com/biojava/biojava-legacy/tree/31ac4dffb733a47b5766cb087aee3aee92e3fcc3/phylo/src/main/java/org/biojavax/bio/phylo/io/phylip
lafita commentedon Nov 13, 2015
The Phylip format can refer to the MSA format, like FASTA format (see here the format explanation) or to a distance matrix format (see here the format explanation). I guess @sbliven that the discussion was about the MSA format. I have seen that forester contains methods to write the DistanceMatrix object as a Phylip format, but I could not find a parser for the MSA format.
In the documentation of their application (see Input and Output Formats section) they do not list PHYLIP as a supported format, but I tried the application and it can read phylip MSA formats, so there must be a parser in the forester package.
Since Phylip seems to be a general format for MSA storage (but less powerful than FASTA), is there a need to provide a parser in the core module of biojava, or using the forester one only for the phylo module is enough? Since we had already an implementation it would be just a design issue.
lafita commentedon Nov 13, 2015
In the forester library:
Probably the GeneralMsaParser class is used to parse Phylip MSA formats (the documentation is poor).
There is also a SymmetricalDistanceMatrixParser class for symmetrical distances in Phylip format.
Merge pull request biojava#122 from Kotlin/website-samples