Many .gde files, particularly those produces by GDE prior to bioLegato, have newlines in the sequence field. For example:

{
name "CACHIT"
type "DNA"
descrip "CACHIT from >CACHIT,, 774 bases, 6B589591 checksum."
direction 1
strandedness 1
sequence "
ATTGCAGTGTATTGGGGACAAAATGGAAATGAAGGGTCTTTGCAAGATGCTTGCAACACA
AACAACTACCAATTTGTGAACATAGCGTTTTTATCCACTTTTGGAAATGGCCAAAACCCA
CAAATAAACCTTGCTGGCCATTGTGATCCATCCACAAATGGCTGCACAAAATTCAGTCCT
GAAATCCAAGCTTGTCAAGCCAAAGGTATCAAAGTGTTGTTGTCGCTCGGAGGCGGAGCA
GGAAGTTACTCTCTGAACTCCGCTGAGGAAGCGACAACACTTGCAAATTACCTTTGGAAC
AATTTCTTGGGTGGCACGTCAACTTCAAGACCATTAGGTGATGCTGTTTTAGATGGAATT
GATTTTGACATTGAATCTGGTGGC---CAACATTATGATGAACTTGCAAAAGCACTT---
---------AATGGTTTT---AGTCAACAGAAAGTTTACCTTTCTGCAGCACCACAATGT
CCTTACCCTGACGCTCATTTGGATTCAGCTATTCAAACTGGTTTATTTGATTATGTTTGG
GTTCAGTTTTATAATAATCCTCAATGTCAATACTCAAATGGAAACATTAACAATCTTGTT
AATGCTTGGAATCAATGGACA---TCAAGTCAAGCTAAACAAGTGTTTTTAGGTGTGCCT
GCTTCTGATGCTGCTGCTCCAAGTGGTGGTTTGATTCCTGCTGATGTTTTGACTTCTCAA
GTTCTTCCTGCTATTAAGACTTCTCCTAAATATGGTGGTGTTATGATTTGGGAT"
}

When bioLegato reads these files, the newlines are included in the alighment, resulting in blank columns in the sequence canvas. Newlines should be stripped from the ends of these sequence lines, as they are for FASTA files.