[BiO BB] Re: Phylogeny trees on many sequences?

[forward at hongyu.org]

To generate a tree for too many sequences, at the first step, just like
you, I use MUSCLE to generate the alignment because it's fast.

Then, I have tried different ways to draw the tree. One is to use the
programs in the Phylip package (or latest EMBOSS/Embassy package) to read
the alignment and draw the phylogenetic tree. Alternatively, I also use
ClustalW to load the alignment and generate the tree because it is easier
to run than Phylip and Phylip has problems with gene names of more than 10
characters. If you generate the alignment using Muscle instead of
ClustalW, you need to insert "CLUSTAL" to the beginning of the first line
of the MUSCLE result when loading it into Clustalw to avoid a format error
message.  Another way that I've tried is to use Java applications such as
Jalview to read the alignment and display the tree.