Hi there,
I have a DNA sample size of 152 sequences with sparse in their length. I want to construct a Maximum likelihood-based phylogenetic tree using PhyML 3.0 but first time it gave me an error about too much "-" in my MSA PHYLIP file format. For that, I replaced all dashes. Again, an error prompted regarding to, for example, "You have an error in your 4 character (F) in species 1". I used other converters and changed MSA Fasta file to PHYLIP file, but all attempt I get those mentioned errors. If I have to equally short all sequences length in PHYLIP file, does it influence my outcome result? Is there any other way to perform tree construction yet save my data intact?
Hi Alireza
In general, I have had good experiences with PhyML 3.0. You need a phylip file and I include an example file for you, which is delivered by PhyML: RDPII_218.phy. I think you will easely be able to get a suitable phylip file for the analysis.
But be careful with gaps "-" in your input file! Poorly aligned regions can be ambiguously aligned and, if you accomodate by yourself, you could violate positional homology. You don't write how long is your alignment but I would recommend you to exclude these regions or, at least, to recode them (hence you lose less information).
Exclusion of poorly aligned regions: I use to exclude poorly aligned regions with Gblocks (http://molevol.cmima.csic.es/castresana/Gblocks.html). This software has the advantage that every one can reproduce the way your alignment has been modified. You need an alignment in fasta format as input file. The calculation is very fast and needs only less RAM. The program can also be applied on a public server mentioned in Castresana's website.
Including ambiguously aligned regions / recoding: I have less experience with it and I know only one method presented in "Lutzoni et al. (2000) Integrating ambiguously aligned regions of DNA sequences in phylogenetic analyses without violating positional homology. Systematic Biology, 49(4), 628-651" I think this recoding method means a lot of work but it would make sense if you have a rather short alignment with few informative positions.
Good luck!
Carolina
Hi dear Carolina
Than you for sharing your exprience. It worked error-free. Alternatively, I used MEGA 5 software package. It needs strong RAM. In this software I performed MSA and fully removed gaps (-).
Bests
Alireza
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