Phylogeny Programs - (Feb/14/2008 )
I have to make a phylogenetic tree. After I align my sequences by ClustalX program, I got a tree file.
But, somebody told me that I have to use PHYLIP to make a tree from ClustalX aln file, it is more reliable than a tree file from ClustalX.
Is it true ? If it is true, I don't understand why a tree file from ClustalX is less reliable.
What is the most favourite phylogeny program and your procedure to make a phylogenetic tree ?
Thank you in advance.
It all has to do with the algorithm that each program uses. Which algorithm is the best is highly argueable and of course it also depends on the type of data you have. The most popular and accepted programs for phylogenetic studies are PHYLIP and PAUP. I tend to prefer PHYLIP's Maximum Likelihood. It will definitely give you more reliable results than Clustal will, but you need to know that your analysis may take a long time to finish (depending on how many sequences you have, their length and other parameters that will make your results more robust, such as bootstrap analysis). Again, the procedure to follow depends on your data. Hope this helps a bit!
this link may be of value
Clustal, now rather old, is know to produce spurious alignments when sequence similarity drops (Sorry Des ). To produce 'good' alignments I would suggest using Muscle - it also produces trees.
To make nice trees, I agree with the previous post - use PAUP, PHYLIP or Mr Bayes.
The question is:
maximum parsimony or maximum liklihood?
<runs for the door>
U are right my supervisor uses Muscle,u can download from here