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', '250']).
(The tree below is shown just as an example of the output; some errant taxa placement is evident).
/--- AF098348_Trictena_atripalpis
/------------------------------------------+
| \--- AF098349_Trictena_sp.
|
| /--- AF098335_Aoraia_lenis
| /---+
| /-------------------------------+ \--- AF098336_Aoraia_rufivena
| | |
| | \------- AF098334_Aoraia_enysii
| |
| /---+ /------------------------------------ AF098347_Oxycanus_sphragidias
| | | |
| | | | /------- AF098346_Oxycanus_antipoda
| | | | /--+
| | | | | | /--- AF098345_Oxycanus_dirempta
| | \--+ /---------------------+ \---+
| | | | | \--- AF098344_Oxycanus_australis
| | | | |
| | | | \---------- AF098343_Jeana_robiginosa
| | | |
| | | | /---------- AF098337_Cladoxycanus_minos
| | \---+ |
| | | /-----------------+ /--- AF098338_Dioxycanus_fuscus
| | | | | /---+
| | | | \--+ \--- AF098339_Dioxycanus_oreas
| | | | |
| | | | \------- AF098342_Heloxycanus_patricki
+ | \---+
| | | /------------------------- AF098340_Dumbletonius_characterifer
| | | |
| | | | /--------------------- AF098351_Wiseana_cervinata
|--+ | | |
| | \--+ | /------- AF098355_Wiseana_jocosa
| | | | /--+
| | | | | | /--- AF098356_Wiseana_mimica
| | | | | \---+
| | \---+ /---+ \--- AF098354_Wiseana_fuliginea
| | | | |
| | | | | /------- AF098359_Wiseana_umbraculata
| | | | \--+
| | | /---+ | /--- AF098357_Wiseana_signata
| | | | | \---+
| | | | | \--- AF098358_Wiseana_signata
| | \--+ |
| | | \-------------- AF098350_Wiseana_cervinata
| | |
| | | /------- AF098341_Dumbletonius_unimaculatus
| | \----------+
| | | /--- AF098353_Wiseana_copularis
| | \---+
| | \--- AF098352_Wiseana_copularis
| |
| \------------------------------------------- AF098333_Aenetus_virescens
|
\---------------------------------------------- AF098332_Fraus_simulans