Edit: The sequences you convert to Phylip format have the same length, because they result from a multiple sequence alignment. Check this site for questions related to "Multiple sequence alignment", or Muscle, ClustalW, MAFFT, etc. Or use one of the web-apps: https://www.ebi.ac.uk/Tools/msa/
EMBOSS' seqret program will do the conversion to phylip if required. Here is the EMBL-EBI web server, which most likely will be sufficient for your aim. Note that Phylip format shortens your sequence identifiers brutally, so you might want to avoid it or shorten your identifiers before conversion.