MalignOnLign

cost of a base substitution
	1	2	3	4	5
. cost of a transversion
	as above	2	3	4	5
. cost of an indel (gap); note: you should set this to be higher than both costs above
	2	3	4	6	8	10

this DNA sequence does not code for a protein and I want the cost of extending a gap to be the same half the cost of the intitial gap

this DNA sequence does code for a protein

to allow for unequal start and end points
---TGCTAT--TGA--
ATATG--ATTCTG---
--AT--TATT-TGACT

to allow for unequal start points only

---TGCTAT--TGACT
ATATG--ATTCTGACT
--AT--TATT-TGACT

to allow for unequal end points only

ATATGCTAT--TGA--
ATATG--ATTCTG---
ATAT--TATT-TGACT

to abuttment

ATATGCTAT--TGACT
ATATG--ATTCTGACT
ATAT--TATT-TGACT

Cost of leading or trailing gaps are not considered in costs of alignment (recommended).

Output Formats

text only (use this for Nona dread)
text only, interleaved
text only, interleaved, and only show differences from first taxon.
Hennig86-ready
Hening86-ready; but gap = 5th state
PAUP-ready
PAUP-ready, and only show differences from first taxon

output in same order as sequences were input (recommended)
write alignment parameter information to output file

Alignment procedure

Hold on to multiple single starting alignment-topologies

No Two Five Ten random reorderings of sequence input.

(branch-breaking / tree-bisection-reconnection) swap on alignments
subtree pruning and regrafting swap on alignments
no swapping (not recommended!)

Keep up to 10 1 5 20 50 100 equally optimal alignments if they are found.

Cost Calculation

topological determination holding multiple trees
topological determination but examining only one tree at a time
simple CLUSTAL-like column-cost, ignoring phylogeny (fast but not recommended)

No Two Five Ten random reorderings of taxa in evaluating alignment.

(branch-breaking / tree-bisection-reconnection) swap on trees
subtree pruning and regrafting swap on trees


Keep up to 10 1 5 20 50 100 equally optimal trees in evaluating alignment