1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
|
# This is a comment
# The first thing in the file must be the Multi-FASTA file
sample.fasta
# The rest of the parameters can be in any order.
# Compound parameters must be on one line.
# Base sequence MUST appear before sequence pairs
# Optional base sequence (default is the first sequence in file).
sample1
# Optional pairs
sample1 sample2
sample1 sample3
sample2 sample3
# MLAGAN parameters
# preceded by "-"
# Phylogenetic tree specification (required).
#-tree "(...)"
-tree "((sample1 sample2) sample3)"
# Lazy evaluation...
#-lazy
# Nested Iterative Refinement
#-nested
# Turning on post-alignment Iterative Refinement
#-postir
# VISTA parameters (defaults)
# preceded by "--"
# ALIGN REGION MIN (75), REGION MAX (100), MIN (50)
#--regmin 75
#--regmax 100
#--min 50
# BASES (10000)
#--bases 10000
# TICK DISTANCE (2000)
#--tickdist 1000
# RESOLUTION (25)
#--resolution 25
# WINDOW (70)
#--window 70
# NUM WINDOWS (4)
#--numwindows 4
|
