Galaxy |

TreeBeST best (version 1.9.2.post0)

Species file in Newick format:

-f

CDS alignment in FASTA format:

Skip PHYML:

(-P)

Ignore the probability of gene evolution (NOT recommended):

(-S)

Apply constraint to PHYML:

(-A)

Discard species that do not appear at all:

(-r)

Constraining tree:

Optional (-C)

Only build tree for genes from sequenced species:

(-s)

Collapse alternative splicing forms:

(-g)

Do not mask low-scoring segments:

(-N)

Quality cut-off:

(-F)

Number of rate categories for PHYML-HKY:

(-c)

tv/ts ratio (kappa):

(-k)

Alpha parameter for Gamma distribution:

(-a)

Duplication probability:

(-d)

Probability of a loss following a speciation:

(-l)

Probability of a loss following a duplication:

(-L)

Probability of the presence of an inconsistent branch:

(-b)

What it does

TreeBeST (gene Tree Building guided by Species Tree) is a versatile program that builds, manipulates and displays phylogenetic trees. It is particularly designed for building gene trees with a known species tree and is highly efficient and accurate.

The 'best' command builds the best gene tree from a species tree and a CDS alignment. The resultant tree will be bootstrapped for 100 times, reconciled with the species tree and rooted by minimizing with the number of duplications and losses. Duplications and losses are also stored in the NHX format.

Note that TreeBeST first determines the topology of resultant tree with a complex procedure, and then performs a hundred times of resampling with an improved neighbour-joining algorithm. Branch lengths are finally estimated with the standard ML method under the HKY model.