These files consist of groups of non-blank lines that look similar to this:
ENTRY G006uaah
TITLE G019uabh 400 bp 240 bases
SEQUENCE
5 10 15 20 25 30
1 A C A T A A A A T A A A C T G T T T T C T A T G T G A A A A
31 T T A A C C T A N N A T A T G C T T T G C T T A T G T T T A
61 A G A T G T C A T G C T T T T T A T C A G T T G A G G A G T
91 T C A G C T T A A T A A T C C T C T A A G A T C T T A A A C
121 A A A T A G G A A A A A A A C T A A A A G T A G A A A A T G
151 G A A A T A A A A T G T C A A A G C A T T T C T A C C A C T
181 C A G A A T T G A T C T T A T A A C A T G A A A T G C T T T
211 T T A A A A G A A A A T A T T A A A G T T A A A C T C C C C
The MEGA format converter looks for the “ENTRY” tag and treats the following string as the sequence name, e.g., G006uaah above. The remaining lines have their digits and spaces removed; any non-sequence characters also are deleted. MEGA would convert the above sequence as follows:
#mega
Title: filename.pir
#G006uaah
ACATAAAATAAACTGTTTTCTATGTGAAAA
TTAACCTANNATATGCTTTGCTTATGTTTA
AGATGTCATGCTTTTTATCAGTTGAGGAGT
TCAGCTTAATAATCCTCTAAGATCTTAAAC
AAATAGGAAAAAAACTAAAAGTAGAAAATG
GAAATAAAATGTCAAAGCATTTCTACCACT
CAGAATTGATCTTATAACATGAAATGCTTT
TTAAAAGAAAATATTAAAGTTAAACTCCCC