2
This is the on-line help file for CLUSTAL W ( version 1.83).
4
It should be named or defined as: clustalw_help
5
except with MSDOS in which case it should be named CLUSTALW.HLP
7
For full details of usage and algorithms, please read the CLUSTALW.DOC file.
10
Toby Gibson EMBL, Heidelberg, Germany.
11
Des Higgins UCC, Cork, Ireland.
12
Julie Thompson IGBMC, Strasbourg, France.
21
Write/Read sequence with range specified. The command line syntax
22
for range specification is flexible. You can use one of the following
29
where m is the starting and m is the length of the sequence.
31
Range and range numbers.
32
=======================
34
Include range numbers in the ouput.
38
The sequence range will be appended as to the names of the sequence.
41
PIM: Percentage Identity Matrix
42
===============================
46
>>HELP 1 << General help for CLUSTAL W (1.81)
48
Clustal W is a general purpose multiple alignment program for DNA or proteins.
50
SEQUENCE INPUT: all sequences must be in 1 file, one after another.
51
7 formats are automatically recognised: NBRF-PIR, EMBL-SWISSPROT,
52
Pearson (Fasta), Clustal (*.aln), GCG-MSF (Pileup), GCG9-RSF and GDE flat file.
53
All non-alphabetic characters (spaces, digits, punctuation marks) are ignored
54
except "-" which is used to indicate a GAP ("." in MSF-RSF).
56
To do a MULTIPLE ALIGNMENT on a set of sequences, use item 1 from this menu to
57
INPUT them; go to menu item 2 to do the multiple alignment.
59
PROFILE ALIGNMENTS (menu item 3) are used to align 2 alignments. Use this to
60
add a new sequence to an old alignment, or to use secondary structure to guide
61
the alignment process. GAPS in the old alignments are indicated using the "-"
62
character. PROFILES can be input in ANY of the allowed formats; just
63
use "-" (or "." for MSF-RSF) for each gap position.
65
PHYLOGENETIC TREES (menu item 4) can be calculated from old alignments (read in
66
with "-" characters to indicate gaps) OR after a multiple alignment while the
67
alignment is still in memory.
70
The program tries to automatically recognise the different file formats used
71
and to guess whether the sequences are amino acid or nucleotide. This is not
74
FASTA and NBRF-PIR formats are recognised by having a ">" as the first
75
character in the file.
77
EMBL-Swiss Prot formats are recognised by the letters
78
ID at the start of the file (the token for the entry name field).
80
CLUSTAL format is recognised by the word CLUSTAL at the beginning of the file.
82
GCG-MSF format is recognised by one of the following:
83
- the word PileUp at the start of the file.
84
- the word !!AA_MULTIPLE_ALIGNMENT or !!NA_MULTIPLE_ALIGNMENT
85
at the start of the file.
86
- the word MSF on the first line of the line, and the characters ..
87
at the end of this line.
89
GCG-RSF format is recognised by the word !!RICH_SEQUENCE at the beginning of
93
If 85% or more of the characters in the sequence are from A,C,G,T,U or N, the
94
sequence will be assumed to be nucleotide. This works in 97.3% of cases
97
>>HELP 2 << Help for multiple alignments
99
If you have already loaded sequences, use menu item 1 to do the complete
100
multiple alignment. You will be prompted for 2 output files: 1 for the
101
alignment itself; another to store a dendrogram that describes the similarity
102
of the sequences to each other.
104
Multiple alignments are carried out in 3 stages (automatically done from menu
105
item 1 ...Do complete multiple alignments now):
107
1) all sequences are compared to each other (pairwise alignments);
109
2) a dendrogram (like a phylogenetic tree) is constructed, describing the
110
approximate groupings of the sequences by similarity (stored in a file).
112
3) the final multiple alignment is carried out, using the dendrogram as a guide.
115
PAIRWISE ALIGNMENT parameters control the speed-sensitivity of the initial
118
MULTIPLE ALIGNMENT parameters control the gaps in the final multiple alignments.
121
RESET GAPS (menu item 7) will remove any new gaps introduced into the sequences
122
during multiple alignment if you wish to change the parameters and try again.
123
This only takes effect just before you do a second multiple alignment. You
124
can make phylogenetic trees after alignment whether or not this is ON.
125
If you turn this OFF, the new gaps are kept even if you do a second multiple
126
alignment. This allows you to iterate the alignment gradually. Sometimes, the
127
alignment is improved by a second or third pass.
129
SCREEN DISPLAY (menu item 8) can be used to send the output alignments to the
130
screen as well as to the output file.
132
You can skip the first stages (pairwise alignments; dendrogram) by using an
133
old dendrogram file (menu item 3); or you can just produce the dendrogram
134
with no final multiple alignment (menu item 2).
137
OUTPUT FORMAT: Menu item 9 (format options) allows you to choose from 6
138
different alignment formats (CLUSTAL, GCG, NBRF-PIR, PHYLIP, GDE, NEXUS, and FASTA).
141
>>HELP 3 << Help for pairwise alignment parameters
142
A distance is calculated between every pair of sequences and these are used to
143
construct the dendrogram which guides the final multiple alignment. The scores
144
are calculated from separate pairwise alignments. These can be calculated using
145
2 methods: dynamic programming (slow but accurate) or by the method of Wilbur
146
and Lipman (extremely fast but approximate).
148
You can choose between the 2 alignment methods using menu option 8. The
149
slow-accurate method is fine for short sequences but will be VERY SLOW for
150
many (e.g. >100) long (e.g. >1000 residue) sequences.
152
SLOW-ACCURATE alignment parameters:
153
These parameters do not have any affect on the speed of the alignments.
154
They are used to give initial alignments which are then rescored to give percent
155
identity scores. These % scores are the ones which are displayed on the
156
screen. The scores are converted to distances for the trees.
158
1) Gap Open Penalty: the penalty for opening a gap in the alignment.
159
2) Gap extension penalty: the penalty for extending a gap by 1 residue.
160
3) Protein weight matrix: the scoring table which describes the similarity
161
of each amino acid to each other.
162
4) DNA weight matrix: the scores assigned to matches and mismatches
163
(including IUB ambiguity codes).
166
FAST-APPROXIMATE alignment parameters:
168
These similarity scores are calculated from fast, approximate, global align-
169
ments, which are controlled by 4 parameters. 2 techniques are used to make
170
these alignments very fast: 1) only exactly matching fragments (k-tuples) are
171
considered; 2) only the 'best' diagonals (the ones with most k-tuple matches)
174
K-TUPLE SIZE: This is the size of exactly matching fragment that is used.
175
INCREASE for speed (max= 2 for proteins; 4 for DNA), DECREASE for sensitivity.
176
For longer sequences (e.g. >1000 residues) you may need to increase the default.
178
GAP PENALTY: This is a penalty for each gap in the fast alignments. It has
179
little affect on the speed or sensitivity except for extreme values.
181
TOP DIAGONALS: The number of k-tuple matches on each diagonal (in an imaginary
182
dot-matrix plot) is calculated. Only the best ones (with most matches) are
183
used in the alignment. This parameter specifies how many. Decrease for speed;
184
increase for sensitivity.
186
WINDOW SIZE: This is the number of diagonals around each of the 'best'
187
diagonals that will be used. Decrease for speed; increase for sensitivity.
190
>>HELP 4 << Help for multiple alignment parameters
192
These parameters control the final multiple alignment. This is the core of the
193
program and the details are complicated. To fully understand the use of the
194
parameters and the scoring system, you will have to refer to the documentation.
196
Each step in the final multiple alignment consists of aligning two alignments
197
or sequences. This is done progressively, following the branching order in
198
the GUIDE TREE. The basic parameters to control this are two gap penalties and
199
the scores for various identical-non-indentical residues.
201
1) and 2) The GAP PENALTIES are set by menu items 1 and 2. These control the
202
cost of opening up every new gap and the cost of every item in a gap.
203
Increasing the gap opening penalty will make gaps less frequent. Increasing
204
the gap extension penalty will make gaps shorter. Terminal gaps are not
207
3) The DELAY DIVERGENT SEQUENCES switch delays the alignment of the most
208
distantly related sequences until after the most closely related sequences have
209
been aligned. The setting shows the percent identity level required to delay
210
the addition of a sequence; sequences that are less identical than this level
211
to any other sequences will be aligned later.
215
4) The TRANSITION WEIGHT gives transitions (A <--> G or C <--> T
216
i.e. purine-purine or pyrimidine-pyrimidine substitutions) a weight between 0
217
and 1; a weight of zero means that the transitions are scored as mismatches,
218
while a weight of 1 gives the transitions the match score. For distantly related
219
DNA sequences, the weight should be near to zero; for closely related sequences
220
it can be useful to assign a higher score.
223
5) PROTEIN WEIGHT MATRIX leads to a new menu where you are offered a choice of
224
weight matrices. The default for proteins in version 1.8 is the PAM series
225
derived by Gonnet and colleagues. Note, a series is used! The actual matrix
226
that is used depends on how similar the sequences to be aligned at this
227
alignment step are. Different matrices work differently at each evolutionary
230
6) DNA WEIGHT MATRIX leads to a new menu where a single matrix (not a series)
231
can be selected. The default is the matrix used by BESTFIT for comparison of
232
nucleic acid sequences.
234
Further help is offered in the weight matrix menu.
237
7) In the weight matrices, you can use negative as well as positive values if
238
you wish, although the matrix will be automatically adjusted to all positive
239
scores, unless the NEGATIVE MATRIX option is selected.
241
8) PROTEIN GAP PARAMETERS displays a menu allowing you to set some Gap Penalty
242
options which are only used in protein alignments.
245
>>HELP A << Help for protein gap parameters.
246
1) RESIDUE SPECIFIC PENALTIES are amino acid specific gap penalties that reduce
247
or increase the gap opening penalties at each position in the alignment or
248
sequence. See the documentation for details. As an example, positions that
249
are rich in glycine are more likely to have an adjacent gap than positions that
252
2) 3) HYDROPHILIC GAP PENALTIES are used to increase the chances of a gap within
253
a run (5 or more residues) of hydrophilic amino acids; these are likely to
254
be loop or random coil regions where gaps are more common. The residues that
255
are "considered" to be hydrophilic are set by menu item 3.
257
4) GAP SEPARATION DISTANCE tries to decrease the chances of gaps being too
258
close to each other. Gaps that are less than this distance apart are penalised
259
more than other gaps. This does not prevent close gaps; it makes them less
260
frequent, promoting a block-like appearance of the alignment.
262
5) END GAP SEPARATION treats end gaps just like internal gaps for the purposes
263
of avoiding gaps that are too close (set by GAP SEPARATION DISTANCE above).
264
If you turn this off, end gaps will be ignored for this purpose. This is
265
useful when you wish to align fragments where the end gaps are not biologically
267
>>HELP 5 << Help for output format options.
269
Six output formats are offered. You can choose any (or all 6 if you wish).
271
CLUSTAL format output is a self explanatory alignment format. It shows the
272
sequences aligned in blocks. It can be read in again at a later date to
273
(for example) calculate a phylogenetic tree or add a new sequence with a
276
GCG output can be used by any of the GCG programs that can work on multiple
277
alignments (e.g. PRETTY, PROFILEMAKE, PLOTALIGN). It is the same as the GCG
278
.msf format files (multiple sequence file); new in version 7 of GCG.
280
PHYLIP format output can be used for input to the PHYLIP package of Joe
281
Felsenstein. This is an extremely widely used package for doing every
282
imaginable form of phylogenetic analysis (MUCH more than the the modest intro-
283
duction offered by this program).
285
NBRF-PIR: this is the same as the standard PIR format with ONE ADDITION. Gap
286
characters "-" are used to indicate the positions of gaps in the multiple
287
alignment. These files can be re-used as input in any part of clustal that
288
allows sequences (or alignments or profiles) to be read in.
290
GDE: this is the flat file format used by the GDE package of Steven Smith.
292
NEXUS: the format used by several phylogeny programs, including PAUP and
295
GDE OUTPUT CASE: sequences in GDE format may be written in either upper or
298
CLUSTALW SEQUENCE NUMBERS: residue numbers may be added to the end of the
299
alignment lines in clustalw format.
301
OUTPUT ORDER is used to control the order of the sequences in the output
302
alignments. By default, the order corresponds to the order in which the
303
sequences were aligned (from the guide tree-dendrogram), thus automatically
304
grouping closely related sequences. This switch can be used to set the order
305
to the same as the input file.
307
PARAMETER OUTPUT: This option allows you to save all your parameter settings
308
in a parameter file. This file can be used subsequently to rerun Clustal W
309
using the same parameters.
311
>>HELP 6 << Help for profile and structure alignments
313
By PROFILE ALIGNMENT, we mean alignment using existing alignments. Profile
314
alignments allow you to store alignments of your favourite sequences and add
315
new sequences to them in small bunches at a time. A profile is simply an
316
alignment of one or more sequences (e.g. an alignment output file from CLUSTAL
317
W). Each input can be a single sequence. One or both sets of input sequences
318
may include secondary structure assignments or gap penalty masks to guide the
321
The profiles can be in any of the allowed input formats with "-" characters
322
used to specify gaps (except for MSF-RSF where "." is used).
324
You have to specify the 2 profiles by choosing menu items 1 and 2 and giving
325
2 file names. Then Menu item 3 will align the 2 profiles to each other.
326
Secondary structure masks in either profile can be used to guide the alignment.
328
Menu item 4 will take the sequences in the second profile and align them to
329
the first profile, 1 at a time. This is useful to add some new sequences to
330
an existing alignment, or to align a set of sequences to a known structure.
331
In this case, the second profile would not be pre-aligned.
334
The alignment parameters can be set using menu items 5, 6 and 7. These are
335
EXACTLY the same parameters as used by the general, automatic multiple
336
alignment procedure. The general multiple alignment procedure is simply a
337
series of profile alignments. Carrying out a series of profile alignments on
338
larger and larger groups of sequences, allows you to manually build up a
339
complete alignment, if necessary editing intermediate alignments.
341
SECONDARY STRUCTURE OPTIONS. Menu Option 0 allows you to set 2D structure
342
parameters. If a solved structure is available, it can be used to guide the
343
alignment by raising gap penalties within secondary structure elements, so
344
that gaps will preferentially be inserted into unstructured surface loops.
345
Alternatively, a user-specified gap penalty mask can be supplied directly.
347
A gap penalty mask is a series of numbers between 1 and 9, one per position in
348
the alignment. Each number specifies how much the gap opening penalty is to be
349
raised at that position (raised by multiplying the basic gap opening penalty
350
by the number) i.e. a mask figure of 1 at a position means no change
351
in gap opening penalty; a figure of 4 means that the gap opening penalty is
352
four times greater at that position, making gaps 4 times harder to open.
354
The format for gap penalty masks and secondary structure masks is explained
355
in the help under option 0 (secondary structure options).
356
>>HELP B << Help for secondary structure - gap penalty masks
358
The use of secondary structure-based penalties has been shown to improve the
359
accuracy of multiple alignment. Therefore CLUSTAL W now allows gap penalty
360
masks to be supplied with the input sequences. The masks work by raising gap
361
penalties in specified regions (typically secondary structure elements) so that
362
gaps are preferentially opened in the less well conserved regions (typically
365
Options 1 and 2 control whether the input secondary structure information or
366
gap penalty masks will be used.
368
Option 3 controls whether the secondary structure and gap penalty masks should
369
be included in the output alignment.
371
Options 4 and 5 provide the value for raising the gap penalty at core Alpha
372
Helical (A) and Beta Strand (B) residues. In CLUSTAL format, capital residues
373
denote the A and B core structure notation. The basic gap penalties are
374
multiplied by the amount specified.
376
Option 6 provides the value for the gap penalty in Loops. By default this
377
penalty is not raised. In CLUSTAL format, loops are specified by "." in the
378
secondary structure notation.
380
Option 7 provides the value for setting the gap penalty at the ends of
381
secondary structures. Ends of secondary structures are observed to grow
382
and-or shrink in related structures. Therefore by default these are given
383
intermediate values, lower than the core penalties. All secondary structure
384
read in as lower case in CLUSTAL format gets the reduced terminal penalty.
386
Options 8 and 9 specify the range of structure termini for the intermediate
387
penalties. In the alignment output, these are indicated as lower case.
388
For Alpha Helices, by default, the range spans the end helical turn. For
389
Beta Strands, the default range spans the end residue and the adjacent loop
390
residue, since sequence conservation often extends beyond the actual H-bonded
393
CLUSTAL W can read the masks from SWISS-PROT, CLUSTAL or GDE format input
394
files. For many 3-D protein structures, secondary structure information is
395
recorded in the feature tables of SWISS-PROT database entries. You should
396
always check that the assignments are correct - some are quite inaccurate.
397
CLUSTAL W looks for SWISS-PROT HELIX and STRAND assignments e.g.
402
The structure and penalty masks can also be read from CLUSTAL alignment format
403
as comment lines beginning "!SS_" or "!GM_" e.g.
405
!SS_HBA_HUMA ..aaaAAAAAAAAAAaaa.aaaAAAAAAAAAAaaaaaaAaaa.........aaaAAAAAA
406
!GM_HBA_HUMA 112224444444444222122244444444442222224222111111111222444444
407
HBA_HUMA VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGK
409
Note that the mask itself is a set of numbers between 1 and 9 each of which is
410
assigned to the residue(s) in the same column below.
412
In GDE flat file format, the masks are specified as text and the names must
413
begin with "SS_ or "GM_.
415
Either a structure or penalty mask or both may be used. If both are included in
416
an alignment, the user will be asked which is to be used.
418
>>HELP C << Help for secondary structure - gap penalty mask output options
420
The options in this menu let you choose whether or not to include the masks
421
in the CLUSTAL W output alignments. Showing both is useful for understanding
422
how the masks work. The secondary structure information is itself very useful
423
in judging the alignment quality and in seeing how residue conservation
424
patterns vary with secondary structure.
427
>>HELP 7 << Help for phylogenetic trees
429
1) Before calculating a tree, you must have an ALIGNMENT in memory. This can be
430
input in any format or you should have just carried out a full multiple
431
alignment and the alignment is still in memory.
434
*************** Remember YOU MUST ALIGN THE SEQUENCES FIRST!!!! ***************
437
The method used is the NJ (Neighbour Joining) method of Saitou and Nei. First
438
you calculate distances (percent divergence) between all pairs of sequence from
439
a multiple alignment; second you apply the NJ method to the distance matrix.
441
2) EXCLUDE POSITIONS WITH GAPS? With this option, any alignment positions where
442
ANY of the sequences have a gap will be ignored. This means that 'like' will be
443
compared to 'like' in all distances, which is highly desirable. It also
444
automatically throws away the most ambiguous parts of the alignment, which are
445
concentrated around gaps (usually). The disadvantage is that you may throw away
446
much of the data if there are many gaps (which is why it is difficult for us to
447
make it the default).
451
3) CORRECT FOR MULTIPLE SUBSTITUTIONS? For small divergence (say <10%) this
452
option makes no difference. For greater divergence, it corrects for the fact
453
that observed distances underestimate actual evolutionary distances. This is
454
because, as sequences diverge, more than one substitution will happen at many
455
sites. However, you only see one difference when you look at the present day
456
sequences. Therefore, this option has the effect of stretching branch lengths
457
in trees (especially long branches). The corrections used here (for DNA or
458
proteins) are both due to Motoo Kimura. See the documentation for details.
460
Where possible, this option should be used. However, for VERY divergent
461
sequences, the distances cannot be reliably corrected. You will be warned if
462
this happens. Even if none of the distances in a data set exceed the reliable
463
threshold, if you bootstrap the data, some of the bootstrap distances may
464
randomly exceed the safe limit.
466
4) To calculate a tree, use option 4 (DRAW TREE NOW). This gives an UNROOTED
467
tree and all branch lengths. The root of the tree can only be inferred by
468
using an outgroup (a sequence that you are certain branches at the outside
469
of the tree .... certain on biological grounds) OR if you assume a degree
470
of constancy in the 'molecular clock', you can place the root in the 'middle'
471
of the tree (roughly equidistant from all tips).
473
5) TOGGLE PHYLIP BOOTSTRAP POSITIONS
474
By default, the bootstrap values are correctly placed on the tree branches of
475
the phylip format output tree. The toggle allows them to be placed on the
476
nodes, which is incorrect, but some display packages (e.g. TreeTool, TreeView
477
and Phylowin) only support node labelling but not branch labelling. Care
478
should be taken to note which branches and labels go together.
480
6) OUTPUT FORMATS: four different formats are allowed. None of these displays
481
the tree visually. Useful display programs accepting PHYLIP format include
482
NJplot (from Manolo Gouy and supplied with Clustal W), TreeView (Mac-PC), and
483
PHYLIP itself - OR get the PHYLIP package and use the tree drawing facilities
484
there. (Get the PHYLIP package anyway if you are interested in trees). The
485
NEXUS format can be read into PAUP or MacClade.
487
>>HELP 8 << Help for choosing a weight matrix
489
For protein alignments, you use a weight matrix to determine the similarity of
490
non-identical amino acids. For example, Tyr aligned with Phe is usually judged
491
to be 'better' than Tyr aligned with Pro.
493
There are three 'in-built' series of weight matrices offered. Each consists of
494
several matrices which work differently at different evolutionary distances. To
495
see the exact details, read the documentation. Crudely, we store several
496
matrices in memory, spanning the full range of amino acid distance (from almost
497
identical sequences to highly divergent ones). For very similar sequences, it
498
is best to use a strict weight matrix which only gives a high score to
499
identities and the most favoured conservative substitutions. For more divergent
500
sequences, it is appropriate to use "softer" matrices which give a high score
501
to many other frequent substitutions.
503
1) BLOSUM (Henikoff). These matrices appear to be the best available for
504
carrying out database similarity (homology searches). The matrices used are:
505
Blosum 80, 62, 45 and 30. (BLOSUM was the default in earlier Clustal W
508
2) PAM (Dayhoff). These have been extremely widely used since the late '70s.
509
We use the PAM 20, 60, 120 and 350 matrices.
511
3) GONNET. These matrices were derived using almost the same procedure as the
512
Dayhoff one (above) but are much more up to date and are based on a far larger
513
data set. They appear to be more sensitive than the Dayhoff series. We use the
514
GONNET 80, 120, 160, 250 and 350 matrices. This series is the default for
515
Clustal W version 1.8.
517
We also supply an identity matrix which gives a score of 1.0 to two identical
518
amino acids and a score of zero otherwise. This matrix is not very useful.
519
Alternatively, you can read in your own (just one matrix, not a series).
521
A new matrix can be read from a file on disk, if the filename consists only
522
of lower case characters. The values in the new weight matrix must be integers
523
and the scores should be similarities. You can use negative as well as positive
524
values if you wish, although the matrix will be automatically adjusted to all
529
For DNA, a single matrix (not a series) is used. Two hard-coded matrices are
533
1) IUB. This is the default scoring matrix used by BESTFIT for the comparison
534
of nucleic acid sequences. X's and N's are treated as matches to any IUB
535
ambiguity symbol. All matches score 1.9; all mismatches for IUB symbols score 0.
538
2) CLUSTALW(1.6). The previous system used by Clustal W, in which matches score
539
1.0 and mismatches score 0. All matches for IUB symbols also score 0.
541
INPUT FORMAT The format used for a new matrix is the same as the BLAST program.
542
Any lines beginning with a # character are assumed to be comments. The first
543
non-comment line should contain a list of amino acids in any order, using the
544
1 letter code, followed by a * character. This should be followed by a square
545
matrix of integer scores, with one row and one column for each amino acid. The
546
last row and column of the matrix (corresponding to the * character) contain
547
the minimum score over the whole matrix.
549
>>HELP 9 << Help for command line parameters
552
-INFILE=file.ext :input sequences.
553
-PROFILE1=file.ext and -PROFILE2=file.ext :profiles (old alignment).
558
-OPTIONS :list the command line parameters
559
-HELP or -CHECK :outline the command line params.
560
-ALIGN :do full multiple alignment
561
-TREE :calculate NJ tree.
562
-BOOTSTRAP(=n) :bootstrap a NJ tree (n= number of bootstraps; def. = 1000).
563
-CONVERT :output the input sequences in a different file format.
566
PARAMETERS (set things)
568
***General settings:****
569
-INTERACTIVE :read command line, then enter normal interactive menus
570
-QUICKTREE :use FAST algorithm for the alignment guide tree
571
-TYPE= :PROTEIN or DNA sequences
572
-NEGATIVE :protein alignment with negative values in matrix
573
-OUTFILE= :sequence alignment file name
574
-OUTPUT= :GCG, GDE, PHYLIP, PIR or NEXUS
575
-OUTORDER= :INPUT or ALIGNED
576
-CASE :LOWER or UPPER (for GDE output only)
577
-SEQNOS= :OFF or ON (for Clustal output only)
578
-SEQNO_RANGE=:OFF or ON (NEW: for all output formats)
579
-RANGE=m,n :sequence range to write starting m to m+n.
581
***Fast Pairwise Alignments:***
583
-TOPDIAGS=n :number of best diags.
584
-WINDOW=n :window around best diags.
585
-PAIRGAP=n :gap penalty
586
-SCORE :PERCENT or ABSOLUTE
589
***Slow Pairwise Alignments:***
590
-PWMATRIX= :Protein weight matrix=BLOSUM, PAM, GONNET, ID or filename
591
-PWDNAMATRIX= :DNA weight matrix=IUB, CLUSTALW or filename
592
-PWGAPOPEN=f :gap opening penalty
593
-PWGAPEXT=f :gap opening penalty
596
***Multiple Alignments:***
597
-NEWTREE= :file for new guide tree
598
-USETREE= :file for old guide tree
599
-MATRIX= :Protein weight matrix=BLOSUM, PAM, GONNET, ID or filename
600
-DNAMATRIX= :DNA weight matrix=IUB, CLUSTALW or filename
601
-GAPOPEN=f :gap opening penalty
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-GAPEXT=f :gap extension penalty
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-ENDGAPS :no end gap separation pen.
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-GAPDIST=n :gap separation pen. range
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-NOPGAP :residue-specific gaps off
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-NOHGAP :hydrophilic gaps off
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-HGAPRESIDUES= :list hydrophilic res.
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-MAXDIV=n :% ident. for delay
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-TYPE= :PROTEIN or DNA
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-TRANSWEIGHT=f :transitions weighting
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***Profile Alignments:***
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-PROFILE :Merge two alignments by profile alignment
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-NEWTREE1= :file for new guide tree for profile1
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-NEWTREE2= :file for new guide tree for profile2
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-USETREE1= :file for old guide tree for profile1
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-USETREE2= :file for old guide tree for profile2
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***Sequence to Profile Alignments:***
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-SEQUENCES :Sequentially add profile2 sequences to profile1 alignment
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-NEWTREE= :file for new guide tree
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-USETREE= :file for old guide tree
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***Structure Alignments:***
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-NOSECSTR1 :do not use secondary structure-gap penalty mask for profile 1
629
-NOSECSTR2 :do not use secondary structure-gap penalty mask for profile 2
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-SECSTROUT=STRUCTURE or MASK or BOTH or NONE :output in alignment file
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-HELIXGAP=n :gap penalty for helix core residues
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-STRANDGAP=n :gap penalty for strand core residues
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-LOOPGAP=n :gap penalty for loop regions
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-TERMINALGAP=n :gap penalty for structure termini
635
-HELIXENDIN=n :number of residues inside helix to be treated as terminal
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-HELIXENDOUT=n :number of residues outside helix to be treated as terminal
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-STRANDENDIN=n :number of residues inside strand to be treated as terminal
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-STRANDENDOUT=n:number of residues outside strand to be treated as terminal
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-OUTPUTTREE=nj OR phylip OR dist OR nexus
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-SEED=n :seed number for bootstraps.
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-KIMURA :use Kimura's correction.
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-TOSSGAPS :ignore positions with gaps.
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-BOOTLABELS=node OR branch :position of bootstrap values in tree display
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>>HELP 0 << Help for tree output format options
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Four output formats are offered: 1) Clustal, 2) Phylip, 3) Just the distances
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None of these formats displays the results graphically. Many packages can
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display trees in the the PHYLIP format 2) below. It can also be imported into
655
the PHYLIP programs RETREE, DRAWTREE and DRAWGRAM for graphical display.
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NEXUS format trees can be read by PAUP and MacClade.
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1) Clustal format output.
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This format is verbose and lists all of the distances between the sequences and
660
the number of alignment positions used for each. The tree is described at the
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end of the file. It lists the sequences that are joined at each alignment step
662
and the branch lengths. After two sequences are joined, it is referred to later
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as a NODE. The number of a NODE is the number of the lowest sequence in that
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2) Phylip format output.
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This format is the New Hampshire format, used by many phylogenetic analysis
668
packages. It consists of a series of nested parentheses, describing the
669
branching order, with the sequence names and branch lengths. It can be used by
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the RETREE, DRAWGRAM and DRAWTREE programs of the PHYLIP package to see the
671
trees graphically. This is the same format used during multiple alignment for
674
Use this format with NJplot (Manolo Gouy), supplied with Clustal W. Some other
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packages that can read and display New Hampshire format are TreeView (Mac/PC),
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TreeTool (UNIX), and Phylowin.
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3) The distances only.
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This format just outputs a matrix of all the pairwise distances in a format
680
that can be used by the Phylip package. It used to be useful when one could not
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produce distances from protein sequences in the Phylip package but is now
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redundant (Protdist of Phylip 3.5 now does this).
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4) NEXUS FORMAT TREE. This format is used by several popular phylogeny programs,
685
including PAUP and MacClade. The format is described fully in:
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Maddison, D. R., D. L. Swofford and W. P. Maddison. 1997.
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NEXUS: an extensible file format for systematic information.
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Systematic Biology 46:590-621.
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5) TOGGLE PHYLIP BOOTSTRAP POSITIONS
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By default, the bootstrap values are placed on the nodes of the phylip format
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output tree. This is inaccurate as the bootstrap values should be associated
693
with the tree branches and not the nodes. However, this format can be read and
694
displayed by TreeTool, TreeView and Phylowin. An option is available to
695
correctly place the bootstrap values on the branches with which they are
added
removed
clustalw_help
