14) How to convert a phylip file to an alignment file

To convert a phylip file to an alignment file:

a) Open the phylip file in BioEdit
b) Go to File\Export\Sequence Alignment
c) Select as type: ClustalW 1.8 (*.aln), name your file and save!!!
d) Since this approach does not provide the sequence conservation line (*, : or .) in the aln file generated, you re-save the file in the aln format using ClustaX: i)Open the aln file from c in ClustaX, ii) File --> Save Sequence as --> Select "CLUSTAL format" under format --> Click on the "OK" button. Now you should be able to see the sequence conservation line.