PATH

Sequences

Protein sequence(s) 1

Paste one protein sequence in FASTA format:

or Upload protein MULTIFASTA file :

Protein sequence(s) 2

Paste one protein sequence in FASTA format:

or Upload protein MULTIFASTA file :

Sequence examples 1 »
Sequence examples 2 »

Parameters

Scoring function

Translation-dependent base substitution scores

Assumed evolutionary distance between sequences: 00.01 00.10 00.30 00.50 00.70 01.00 01.50 02.00 empirical mutations per codon (more information about the translation dependent scores)

Classic base substitution scores

Match: Transversion mutation: Transition mutation:

Gap penalties

Gap of size 3 (codon insertion or deletion):

opening: extension:

Frameshift gap (insertion/deletion of one or two bases):

opening: extension:

Alignment sense

Forward (align the first sequence with the second sequence, both in the forward translation sense)
Backward (align the first sequence with the reverse complementary of the second sequence)
Forward and Backward