Irwin Jungreis

No, a single sequence is not sufficient for PhyloCSF. PhyloCSF gets most of its information from substitutions between different species. If you give it a single sequence, it will give...

PhyloCSF does not make explicit use of the genetic code, but the information is implicit in the data used to train the coding and non-coding models. In addition to having...

I would guess that such transcripts would look like lncRNAs, transcribed and spliced in the nucleus before heading to the mitochondrion for translation. I'd expect that most of their codons...

Since Mike hasn't responded... One approach would be to use the PhyloCSF Omega method, which does not require a precomputed ECM model: https://github.com/mlin/PhyloCSF/wiki/Omega-Test This is slower and not as accurate...

PhyloCSF is intended to be used on many-species alignments, such as 12-flies or 29-mammals. As far as I know, it has never been used on alignments of only two species,...

PhyloCSF requires a multi-species alignment of species in the right range of genomic distance (for example, 29 placental mammals). I am not aware of such an alignment for sharks. Do...

Creating your own alignments is theoretically possible, though it would be a lot of work (and I'm not an expert in that so I couldn't help you). The smallest tree...

The file name should be "12flies" not "12files". On Jun 20, 2013, at 1:52 PM, Jhon.Chang wrote: > Yeah,I have already compiled successfully on ubuntu 13.04. I'm very exciting now....