Trimming trees with TreeBeST

I needed a program that can easily trim branches from a phylogenetic tree and came across TreeBeST (Tree Building guided by Species Tree). TreeBeST is a neat and versatile program that builds, manipulates and displays phylogenetic trees and seems to be perfect for the job.

TreeBeST with Ensembl Compara modifications is available at SBo and requires only fltk. The SlackBuild installs the command line treebest and its graphical front-end fltreebest. Let’s say we have a list of species, for which I have obtained a phylogenetic tree from TreeTime:

The program can save trees in *.nhx format with line breaks:

(Danio_rerio:435.324,
(Xenopus_tropicalis:351.758,
((Anolis_carolinensis:279.657,
(((Gallus_gallus:79.9554,
Anas_platyrhynchos:79.9554
)'14':18.0875,
Geospiza_fortis:98.0429
)'13':155.691,
Chelonia_mydas:253.734
)'11':25.9228
)'10':32.2469,
(((((Orcinus_orca:55.9599,
Bos_taurus:55.9599
)'19':6.00614,
Sus_scrofa:61.966
)'9':34.4964,
((Cavia_porcellus:72.8767,
(Rattus_norvegicus:20.8874,
Mus_musculus:20.8874
)'22':51.9893
)'8':16.9465,
(Gorilla_gorilla:9.0631,
(Pan_troglodytes:6.6509,
Homo_sapiens:6.6509
)'6':2.41219
)'30':80.7601
)'29':6.6392
)'27':8.99739,
Loxodonta_africana:105.46
)'35':71.4677,
Ornithorhynchus_anatinus:176.927
)'43':134.976
)'42':39.8546
)'40':83.5656
);

If I want to remove the sea mammal Orcinus orca (killer whale), I can use the command line treebest. First, prepare an updated species list, where O. orca is removed:

Anolis_carolinensis
Cavia_porcellus
Danio_rerio
Gallus_gallus
Homo_sapiens
Loxodonta_africana
Mus_musculus
Ornithorhynchus_anatinus
Pan_troglodytes
Rattus_norvegicus
Sus_scrofa
Xenopus_tropicalis
Gorilla_gorilla
Anas_platyrhynchos
Geospiza_fortis
Bos_taurus
Chelonia_mydas

Then run treebest with the subtree option, pointing the input tree (species.nhx) and the list of trimmed species (species-trim.txt):

treebest subtree species.nhx species-trim.txt > trimmedTree.nhx

This outputs the subtree file trimmedTree.nhx with node ’19’ gone:

(Danio_rerio:435.324,
(Xenopus_tropicalis:351.758,
((Anolis_carolinensis:279.657,
(((Gallus_gallus:79.9554,
Anas_platyrhynchos:79.9554
)'14':18.0875,
Geospiza_fortis:98.0429
)'13':155.691,
Chelonia_mydas:253.734
)'11':25.9228
)'10':32.2469,
((((Bos_taurus:61.966,
Sus_scrofa:61.966
)'9':34.4964,
((Cavia_porcellus:72.8767,
(Rattus_norvegicus:20.8874,
Mus_musculus:20.8874
)'22':51.9893
)'8':16.9465,
(Gorilla_gorilla:9.0631,
(Pan_troglodytes:6.6509,
Homo_sapiens:6.6509
)'6':2.41219
)'30':80.7601
)'29':6.6392
)'27':8.99739,
Loxodonta_africana:105.46
)'35':71.4677,
Ornithorhynchus_anatinus:176.927
)'43':134.976
)'42':39.8546
)'40':83.5656
);

Great!