Using DendroPy Interoperability Modules to Download, Align, and Estimate a Tree from GenBank Sequences

The following example shows how easy it can be to use the three interoperability modules provided by the DendroPy Phylogenetic Computing Library to download nucleotide sequences from GenBank, align them using MUSCLE, and estimate a maximum-likelihood tree using RAxML. The automatic label composition option of the DendroPy genbank module creates practical taxon labels out the original data. We also pass in additional arguments to RAxML to request that the tree search be carried out 250 times (['-N', Read more [...]

Molecular Sequence Generation with DendroPy

The DendroPy Phylogenetic Computing Library includes native infrastructure for phylogenetic sequence simulation on DendroPy trees under the HKY model. Being pure-Python, however, it is a little slow. If Seq-Gen is installed on your system, though, you can take advantage of a lightweight Seq-Gen wrapper added to the latest revision under the interop subpackage: dendropy.interop.seqgen. Documentation is lagging, but the following examples should be enough to get started, and the class is simple and Read more [...]

Download Sequences from GenBank, Keeping Only Codons

The following script takes a space separated list of GenBank numbers as input, and then uses BioPython to download the corresponding sequences from GenBank, strips off all non-coding nucleotides, gives the sequences sensible names, and assembles them into a FASTA file. It is pretty basic, and does not do a lot of fancy error checking, and is probably a little too specific to be useful for most people. I can imagine extending it in a number of ways that would make it much more useful in a number Read more [...]