Converting the PHYLIP interleaved file format
The PHYLIP format is interleaved, similar to the MSF format. It consists of a line of numeric data, which is ignored by MEGA, followed by a group of one or more lines of text. The text begins with a sequence name in the first column and is followed by the initial part of each sequence; the group is terminated by a blank line. The number of lines in subsequent groups of data is similar to the first group. Each line is a continuation of the identified sequence and begins in the same position as in the first group. The following might be observed at the beginning of a PHYLIP data file:
2 2000 I
G019uabh ATACATCATA ACACTACTTC CTACCCATAA GCTCCTTTTA ACTTGTTAAA
G028uaah CATAAGCTCC TTTTAACTTG TTAAAGTCTT GCTTGAATTA AAGACTTGTT
GTCTTGCTTG AATTAAAGAC TTGTTTAAAC ACAAAAATTT AGAGTTTTAC
TAAACACAAA ATTTAGACTT TTACTCAACA AAAGTGATTG ATTGATTGAT
TCAACAAAAG TGATTGATTG ATTGATTGAT TGATTGATGG TTTACAGTAG
TGATTGATTG ATGGTTTACA GTAGGACTTC ATTCTAGTCA TTATAGCTGC
MEGA would convert this data as follows:
#mega
Title: cap-data.phylip
#G019uabh
ATACATCATA ACACTACTTC CTACCCATAA GCTCCTTTTA ACTTGTTAAA
GTCTTGCTTG AATTAAAGAC TTGTTTAAAC ACAAAAATTT AGAGTTTTAC
TCAACAAAAG TGATTGATTG ATTGATTGAT TGATTGATGG TTTACAGTAG
#G028uaah
CATAAGCTCC TTTTAACTTG TTAAAGTCTT GCTTGAATTA AAGACTTGTT
TAAACACAAA ATTTAGACTT TTACTCAACA AAAGTGATTG ATTGATTGAT
TGATTGATTG ATGGTTTACA GTAGGACTTC ATTCTAGTCA TTATAGCTGC