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Sequence trees were constructed using Phyml [ 127].
There is much phylogenetic evidence other than sequence trees; phylogenetic arguments entirely independent of sequence trees can often be stronger than the conclusions of a sequence tree.
Protein sequence trees were constructed from template CLUSTALX tree files (.ph) generated during MCOFFEE alignment.
So clustering algorithms might tend to cluster longer sequence trees together, due to their higher similarity.
The term was invented a century before anyone did sequence trees or invented electronic computers.
Besides placement on sequence trees, there are three major areas where archaea and bacteria differ greatly.
Sequence trees are unrooted and thus useless to distinguish between chlorobacteria being paraphyletic or holophyletic.
Yet such fundamental questions are typically ignored through preoccupation with sequence trees and genes alone [ 177].
These severe limitations of sequence trees emphatically do not mean that they are worthless.
For construction of protein sequence trees, bootstrap resampling was performed using SEQBOOT.
For each data set, we performed 20 replicates of a TBR local search heuristic starting with random addition sequence trees.
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