clustalw.doc

在任务级并行平台P2HP上

The New Hampshire format is only useful if you have software to display or
manipulate the trees.  The PHYLIP package is highly recommended if you intend
to do much work with trees and includes programs for doing this.  If you do
not have such software, request the trees in the older clustal format
and see the documentation for Clustal V (clustalv.doc).  WE DO NOT PROVIDE
ANY DIRECT MEANS FOR VIEWING TREES GRAPHICALLY.

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4) THE ALIGNMENT ALGORITHMS


The basic algorithm is the same as for Clustal V and is described in some
detail in clustalv.doc.  The new modifications are described in detail in 
clustalw.ms.  Here we just list some notes to help answer some of the most
obvious questions.


Terminal Gaps

In the original Clustal V program, terminal gaps were penalised the same
as all other gaps.  This caused some ugly side effects e.g.

acgtacgtacgtacgt                              acgtacgtacgtacgt
a----cgtacgtacgt  gets the same score as      ----acgtacgtacgt

NOW, terminal gaps are free.  This is better on average and stops silly
effects like single residues jumping to the edge of the alignment.  However,
it is not perfect.  It does mean that if there should be a gap near the end 
of the alignment, the program may be reluctant to insert it i.e. 

cccccgggccccc                                              cccccgggccccc
ccccc---ccccc  may be considered worse (lower score) than  cccccccccc---

In the right hand case above, the terminal gap is free and may score higher
than the laft hand alignment.  This can be prevented by lowering the gap
opening and extension penalties.   It is difficult to get this right all the
time.  Please watch the ends of your alignments. 



Speed of the initial (pairwise) alignments (fast approximate/slow accurate)

By default, the initial pairwise alignments are now carried out using a full
dynamic programming algorithm.  This is more accurate than the older hash/
k-tuple based alignments (Wilbur and Lipman) but is MUCH slower.  On a fast
workstation you may not notice but on a slow box, the difference is extreme.
You can set the alignment method from the menus easily to the older, faster
method.



Delaying alignment of distant sequences

The user can set a cut off to delay the alignment of the most divergent
sequences in a data set until all other sequences have been aligned.  By 
default, this is set to 40% which means that if a sequence is less than 40%
identical to any other sequence, its alignment will be delayed.  



Iterative realignment/Reset gaps between alignments

By default, if you align a set of sequences a second time (e.g. with changed
gap penalties), the gaps from the first alignment are discarded.  You can
set this from the menus so that older gaps will be kept between alignments,
This can sometimes give better alignments by keeping the gaps (do not reset
them) and doing the full multiple alignment a second time.  Sometimes, the
alignment will converge on a better solution; sometimes the new alignment will
be the same as the first.  There can be a strange side effect: you can get
columns of nothing but gaps introduced.  

Any gaps that are read in from the input file are always kept, regardless 
of the setting of this switch.  If you read in a full multiple alignment, the "reset
gaps" switch has no effect.  The old gaps will remain and if you carry out 
a multiple alignment, any new gaps will be added in.  If you wish to carry out 
a full new alignment of a set of sequences that are already aligned in a file
you must input the sequences without gaps.



Profile alignment

By profile alignment, we simply mean the alignment of old alignments/sequences.
In this context, a profile is just an existing alignment (or even a set of 
unaligned sequences; see below).  This allows you to
read in an old alignment (in any of the allowed input formats) and align
one or more new sequences to it.  From the profile alignment menu, you
are allowed to read in 2 profiles.  Either profile can be a full alignment
OR a single sequence.  In the simplest mode, you simply align the two profiles
to each other. This is useful if you want to gradually build up a full
multiple alignment.  

A second option is to align the sequences from the second profile, one at
a time to the first profile.  This is done, taking the underlying tree between
the sequences into account.  This is useful if you have a set of new sequences
(not aligned) and you wish to add them all to an older alignment.

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5) CHANGES TO THE PHYLOGENTIC TREE CALCULATIONS AND SOME HINTS.



IMPROVED DISTANCE CALCULATIONS FOR PROTEIN TREES


The phylogenetic trees in Clustal W (the real trees that you calculate
AFTER alignment; not the guide trees used to decide the branching order
for multiple alignment) use the Neighbor-Joining method of Saitou and
Nei based on a matrix of "distances" between all sequences.  These distances
can be corrected for "multiple hits".  This is normal practice when accurate
trees are needed.  This correction stretches distances (especially large ones)
to try to correct for the fact that OBSERVED distances (mean number of 
differences per site) greatly underestimate the actual number that happened
during evolution.  

In Clustal V we used a simple formula to convert an observed distance to one
that is corrected for multiple hits.  The observed distance is the mean number
of differences per site in an alignment (ignoring sites with a gap) and is
therefore always between 0.0 (for ientical sequences) an 1.0 (no residues the
same at any site).  These distances can be multiplied by 100 to give percent
difference values.  100 minus percent difference gives percent identity.
The formula we use to correct for multiple hits is from Motoo Kimura
(Kimura, M. The neutral Theory of Molecular Evolution, Camb.Univ.Press, 1983,
page 75) and is:

K = -Ln(1 - D - (D.D)/5)  where D is the observed distance and K is       
                              corrected distance.

This formula gives mean number of estimated substitutions per site and, in
contrast to D (the observed number), can be greater than 1 i.e. more than
one substitution per site, on average.  For example, if you observe 0.8
differences per site (80% difference; 20% identity), then the above formula
predicts that there have been 2.5 substitutions per site over the course 
of evolution since the 2 sequences diverged.  This can also be expressed in 
PAM units by multiplying by 100 (mean number of substitutions per 100 residues).
The PAM scale of evolution and its derivation/calculation comes from the
work of Margaret Dayhoff and co workers (the famous Dayhoff PAM series
of weight matrices also came from this work).  Dayhoff et al constructed
an elaborate model of protein evolution based on observed frequencies
of substitution between very closely related proteins.  Using this model,
they derived a table relating observed distances to predicted PAM distances.
Kimura's formula, above, is just a "curve fitting" approximation to this table.
It is very accurate in the range 0.75 > D > 0.0 but becomes increasingly
unaccurate at high D (>0.75) and fails completely at around D = 0.85.

To circumvent this problem, we calculated all the values for K corresponding
to D above 0.75 directly using the Dayhoff model and store these in an 
internal table, used by Clustal W.  This table is declared in the file dayhoff.h and
gives values of K for all D between 0.75 and 0.93 in intervals of 0.001 i.e.
for D = 0.750, 0.751, 0.752 ...... 0.929, 0.930.   For any observed D 
higher than 0.930, we arbitrarily set K to 10.0.  This sounds drastic but
with real sequences, distances of 0.93 (less than 7% identity) are rare.
If your data set includes sequences with this degree of divergence, you
will have great difficulty getting accurate trees by ANY method; the alignment
itself will be very difficult (to construct and to evaluate).

There are some important
things to note.  Firstly, this formula works well if your sequences are
of average amino acid composition and if the amino acids substitute according
to the original Dayhoff model.  In other cases, it may be misleading.  Secondly,
it is based only on observed percent distance i.e. it does not DIRECTLY
take conservative substitutions into account.  Thirdly, the error on the
estimated PAM distances may be VERY great for high distances; at very high
distance (e.g. over 85%) it may give largely arbitrary corrected distances.
In most cases, however, the correction is still worth using; the trees will
be more accurate and the branch lengths will be more realistic.  

A far more sophisticated distance correction based on a full Dayhoff
model which DOES take conservative substitutions and actual amino acid
composition into account, may be found in the PROTDIST program of the
PHYLIP package.  For serious tree makers, this program is highly recommended. 



TWO NOTES ON BOOTSTRAPPING...

When you use the BOOTSTRAP in Clustal W to estimate the reliability of parts
of a tree, many of the uncorrected distances may randomly exceed the arbitrary cut
off of 0.93 (sequences only 7% identical) if the sequences are distantly
related.  This will happen randomly i.e. even if none of the pairs of 
sequences are less than 7% identical, the bootstrap samples may contain pairs
of sequences that do exceed this cut off.
If this happens, you will be warned.  In practice, this can
happen with many data sets.  It is not a serious problem if it happens rarely.
If it does happen (you are warned when it happens and told how often the
problem occurs), you should consider removing the most distantly
related sequences and/or using the PHYLIP package instead.


A further problem arises in almost exactly the opposite situation: when
you bootstrap a data set which contains 3 or more sequences that are identical
or almost identical.  Here, the sets of identical sequences should be shown
as a multifurcation (several sequences joing at the same part of the tree).
Because the Neighbor-Joining method only gives strictly dichotomous trees
(never more than 2 sequences join at one time), this cannot be exactly 
represented.  In practice, this is NOT a problem as there will be some
internal branches of zero length seperating the sequences.  If you
display the tree with all branch lengths, you will still see a multifurcation.  
However, when you bootstrap
the tree, only the branching orders are stored and counted.  In the case
of multifurcations, the exact branching order is arbitrary but the program
will always get the same branching order, depending only on the input order
of the sequences.  In practice, this is only a problem in situations where
you have a set of sequences where all of them are VERY similar.  In this case,
you can find very high support for some groupings which will disappear if you
run the analysis with a different input order.  Again, the PHYLIP package
deals with this by offering a JUMBLE option to shuffle the input order
of your sequences between each bootstrap sample.  

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6) SUMMARY OF THE COMMAND LINE USAGE

Clustal W is designed to be run interactively.  However, there are many 
situations where it is convenient to run it from the command line, especially
if you wish to run it from another piece of software (e.g. SeqApp or GDE).
All parameters can be set from the command line by giving options after the
clustalw command. On UNIX options should be preceded by '-', all other systems
use the '/' character.

If anything is put on the command line, the program will (attempt to) carry
out whatever is requested and will exit.  If you wish to use the command
line to set some parameters and then go into interactive mode, use the
command line switch: interactive .... e.g.

clustalw -quicktree -interactive    on UNIX
or
clustalw /quicktree /interactive    on VMS,MAC and PC

will set the default initial alignment mode to fast/approximate and will then
go to the main menu.


To see a list of all the command line parameters, type: 

clustalw -options           on UNIX
or
clustalw /options           on VMS,MAC and PC

and you will see a list with no explanation.


To get (VERY BRIEF) help on command line usage, use the /HELP or /CHECK
(-help or -check on UNIX systems) options.  Otherwise, the command line
usage is self explanatory or is explained in clustalv.doc.  The defaults
for all parameters are set in the file param.h which can be changed easily 
(remember to recompile the program afterwards :-).

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