|
Value
option |
Legal
values |
Default |
Description |
|
anchorspacing |
Integer |
32 |
Minimum spacing between anchor columns.
|
|
center |
Floating point |
[1] |
Center parameter. Should be negative.
|
|
cluster1
cluster2 |
upgma
upgmb
neighborjoining |
upgmb |
Clustering method. cluster1 is used in iteration 1
and 2, cluster2 in later iterations.
|
|
clwout |
File name |
None |
Write output in CLUSTALW format to given file
name. |
|
clwout |
File name |
None |
As -clwout, except that header is strictly
compatible with CLUSTALW 1.81.
|
|
diagbreak |
Integer |
1 |
Maximum distance between two
diagonals that allows them to merge into one diagonal.
|
|
diaglength |
Integer |
24 |
Minimum length of diagonal.
|
|
diagmargin |
Integer |
5 |
Discard this many positions at ends of diagonal.
|
|
distance1
|
kmer6_6
kmer20_3
kmer20_4
kbit20_3
kmer4_6
|
Kmer6_6 (amino)
or Kmer4_6 (nucleo) |
Distance measure for
iteration 1. |
|
distance2
|
pctidkimura
pctidlog
|
pctidkimura |
Distance measure for
iterations 2, 3 ...
|
|
fastaout |
File name |
None |
Write output in FASTA format
to the given file.
|
|
gapopen |
Floating point |
[1] |
The gap open score. Must be
negative.
|
|
hydro |
Integer |
5 |
Window size for determining
whether a region is hydrophobic.
|
|
hydrofactor |
Floating point |
1.2 |
Multiplier for gap open/close
penalties in hydrophobic regions.
|
|
in |
Any file name |
standard input |
Where to find the input
sequences.
|
|
in1 |
Any file name |
None |
Where to find an input
alignment.
|
|
in2 |
Any file name |
None |
Where to find an input
alignment.
|
|
log |
File name |
None. |
Log file name (delete
existing file).
|
|
loga |
File name |
None. |
Log file name (append to
existing file).
|
|
matrix |
File name |
None |
File name for substitution
matrix in NCBI or WU-BLAST format. If you specify your own matrix, you
should also specify:
-gapopen <g>, -gapextend <e>
-center 0.0
Note that <g> and <e> MUST be
negative.
|
|
maxhours |
Floating point |
None. |
Maximum time to run in hours.
The actual time may exceed the requested limit by a few minutes.
Decimals are allowed, so 1.5 means one hour and 30 minutes.
|
|
maxiters |
Integer 1, 2 ... |
16 |
Maximum number of iterations.
|
|
maxtrees |
Integer |
1 |
Maximum number of new trees
to build in iteration 2.
|
|
minbestcolscore |
Floating point |
[1] |
Minimum score a column must have to be an anchor.
|
|
minsmoothscore |
Floating point |
[1] |
Minimum smoothed score a column must have to be an
anchor.
|
|
msaout |
File name |
None |
Write output to given file name in MSF format.
|
|
objscore |
sp
ps
dp
xp
spf
spm |
spm |
Objective score used by tree
dependent refinement.
sp=sum-of-pairs score.
spf=sum-of-pairs score (dimer
approximation)
spm=sp for < 100 seqs,
otherwise spf
dp=dynamic programming score.
ps=average profile-sequence
score.
xp=cross profile score.
|
|
out |
File name |
standard output |
Where to write the alignment.
|
|
phyiout |
File name |
None |
Write output in Phylip
interleaved format to given file name.
|
|
physout |
File name |
None |
Write output in Phylip
sequential format to given file name.
|
|
refinewindow |
Integer |
200 |
Length of window for
-refinew.
|
|
root1
root2 |
pseudo
midlongestspan
minavgleafdist |
psuedo |
Method used to root tree;
root1 is used in iteration 1 and 2, root2 in later iterations.
|
|
scorefile |
File name |
None |
File name where to write a
score file. This contains one line for each column in the alignment. The
line contains the letters in the column followed by the average BLOSUM62
score over pairs of letters in the column.
|
|
seqtype |
protein
dna
rna
auto
|
auto |
Sequence type. |
|
smoothscoreceil |
Floating point |
[1] |
Maximum value of column score
for smoothing purposes.
|
|
smoothwindow |
Integer |
7 |
Window used for anchor column
smoothing.
|
|
spscore |
File name |
|
Compute SP objective score of
multiple alignment.
|
|
SUEFF |
Floating point value between
0 and 1.
|
0.1 |
Constant used in UPGMB
clustering. Determines the relative fraction of average linkage (SUEFF)
vs. nearest-neighbor linkage (1 – SUEFF).
|
|
tree1
tree2 |
File name |
None |
Save tree produced in first
or second iteration to given file in Newick (Phylip-compatible) format.
|
|
usetree |
File name |
None |
Use given tree as guide tree.
Must by in Newick (Phyip-compatible) format.
|
|
weight1
weight2 |
none
henikoff
henikoffpb
gsc
clustalw
threeway |
clustalw
|
Sequence weighting scheme.
weight1 is used in iterations 1 and 2.
weight2 is used for tree-dependent refinement.
none=all sequences have equal weight.
henikoff=Henikoff & Henikoff weighting scheme.
henikoffpb=Modified Henikoff scheme as used in
PSI-BLAST.
clustalw=CLUSTALW method.
threeway=Gotoh three-way method.
|