... help . ... Fixed two bugs in one place: base Alignment /Block - realign used to cut sequence tails if the new alignment was wider than the existing one - any block modification that added new columns used to forget to add the columns to the alignment AFAIR, currently the only such modifications are IO, append_*, and realign() To fix it I've: - changed realign to use _pad_to_width ... 2 import subprocess . 3 import os . ... add_option ( '-n' , '--size' , type = int , help = 'Pool size' ) . ...