I have 737 sequences that aligned with MAFFT, then Gblock removed poor position, and PhyML was used to determine the model and drawing of the tree.
I have problems with the use of PhyML in http://www.atgc-montpellier.fr/phyml/:
if the number of characters of accession number was more than 10, full name of accession is not display at tree.
I have 737 sequences that do not represent all in the tree. The number of output files for me gives 4 files.
Remove empty spaces and special characters other than . _ - in fasta header.
If not working, use fasttree for making phylogenetic tree.
You can short the name of the sequences the way Abhijeet Singh has suggested and run PhyML.
If you have identical sequences after the MAFFT/Gblock steps, PhyML would remove the redundancy and keep only one representative sequence, so the number of sequences in the output would be fewer that in the input
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