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choice.NucleicAcidsResearch,22:
4673-4680.
--------------------------------------------------------------
What'
sNew（March1996）inVersion1.6（sinceversion1.5）.
1）Improvedhandlingofsequencesofunequallength.Previously,we
increasedthegapextensionpenaltiesforbothsequencesifthetwosequences
（orgroupsofpreviouslyalignedsequences）wereofdifferentlengths.
Now,weincreasethegapopeningandextensionpenaltiesfortheshorter
sequenceonly.Thishelpspreventshortsequencesbeingstretchedout
alonglongerones.
2）Addedthe"
Gonnet"
seriesofweightmatrices（fromGastonGonnetand
co-workersattheETHinZurich）.Fixedabuginthematrix
choicemenu;
nowPAMmatricescanbeselectedok.
3）Addedsecondarystructure/gappenaltymasks.Theseallowyouto
include,inanalignment,apositionspecificsetofgappenalties.
Youcaneithersetagapopeningpenaltyateachpositionorspecify
thesecondarystrcuture（ifprotein;
alphahelix,betastrandorloop）
andhavegappenaltiessetautomatically.This,basically,isusedtomake
gapshardertoopeninsidehelicesorstrands.
Thesemasksareonlyusedinthe"
profilealignment"
menu.Theymaybereadin
aspartofanalignmentinaspecialformat（seetheon-linehelpfor
details）orassociatedwitheachsequence,ifthesequencesareinSwissProt
formatandsecondarystructureinformationisgiven.Allofthemask
parameterscanbesetfromtheprofilealignmentmenu.Basically,the
maskismadeupofaseriesofnumbersbetween1and9,oneperposition.
Thegapopeningpenaltyatapositioniscalculatedasthestartingpenalty
multipleiedbythemaskvalueatthatsite.
4）Addedcommandlineoptions/profileand/sequences.
Theseallowusestochoosebetweennormalprofilealignmentwherethe
twoprofiles（pre-existingalignmentsspecifiedinthefiles
/profile1=and/profile2=）aremerged/alignedwitheachother（/profile）
andthecasewheretheindividualsequencesin/profile2arealigned
sequentiallywiththealignmentin/profile1（/sequences）.
5）FixedbuginmodifiedMyersandMilleralgorithm-gappenaltyscore
wasnotalwayscalculatedproperlyfortype2midpoints.Thisisthecore
alignmentalgorithm.
6）Onlyallowsoneoutputfileformattobeselectedfromcommandline
-ie.multipleoutputalignmentfilesarenotallowed.
7）Fixed'
badcallstockfree'
errorduringcalculationofphylipdistance
matrix.
8）Fixedcommandlineoptions/gapopen/gapext/type=protein/negative.
9）AllowedusertochangecommandlineseparatoronUNIXfrom'
/'
to'
-'
.
Thisallowsunixuserstousethemoreconventinal'
symbol
forseperatingcommandlineoptions."
/"
canthenbeusedinunix
filenamesonthecommandline.Thesymbolthatisused,
isspecifiedinthefileclustalw.hwhichmustbeeditedifyou
wishtochangeit（andtheprogrammustthenberecompiled）.Findthe
blockofcodeinclustalw.hthatcorrspondstotheoperatingsystemyou
areusing.Theseblocksarestartedbyoneofthefollowing:
#ifdefVMS
#elifMAC
#elifMSDOS
#elifUNIX
Onthenextlineaftereachistheline:
#defineCOMMANDSEP'
Changethisintheappropriateblockofcode（e.g.theUNIXblock）to
ifyouwishtousethe"
-"
characterascommandseperator.
sNew（April1995）inVersion1.5（sinceversion1.3）.
1）portedtoMACandPC.Theseversionsarequiteslowunlessyou
haveanicebeefymachine.OnaPowerMacoraPentiumbox
itisniceandfast.TwoprecompiledversionsaresuppliedforMacs
（Powermacandoldmacversions）.
Mac:
1500residuesby100sequences
PowerMac3000"
"
PC1500"
2）alignmentofnewsequencestoanalignment.Fixedaseriousbug
whichassignedweightstothewrongsequences.Nowalso,weights
sequencesaccordingtodistancefromtheincomingsequence.The
newweightsare:
treeweights*similaritytoincomingsequence.
Thetreeweightsaretheoldweightsthatwederivefromthetree
connectingallthesequencesintheexistingalignment.
3）forallplatforms,outputlinelength=60.
4）Bootstrapfiles（*.phb）:
the"
final"
node（arbitrarytrichotomy
attheendoftheneighbor-joiningprocess）islabelledas
TRICHOTOMYinthebootstrapoutputfiles.Thisistohelp
linkbootstrapfigureswithnodeswhenyourerootthetree.
5）Commandline/bootstrapoptionnowmorerobust.
INTRODUCTION
ThisdocumentgivessomeBRIEFnotesaboutusageoftheClustalW
multiplealignmentprogramforUNIXandVMSmachines.ClustalW
isamajorupdateandrewriteoftheClustalVprogramwhich
wasdescribedin:
Higgins,D.G.,Bleasby,A.J.andFuchs,R.（1992）
CLUSTALV:
improvedsoftwareformultiplesequencealignment.
ComputerApplicationsintheBiosciences（CABIOS）,8
（2）:
189-191.
Themainnewfeaturesareagreatlyimproved（moresensitive）
multiplealignmentprocedureforproteinsandimprovedsupport
fordifferentfileformats.Thissoftwarewasdescribedin:
improvingthesensitivityofprogressivemultiple
sequencealignmentthroughsequenceweighting,positionspecific
gappenaltiesandweightmatrixchoice.
NucleicAcidsResearch,22（22）:
TheusageofClustalWislargelythesameasfor
ClustalVdetailsofwhicharedescribedinclustalv.doc.Detailsofthe
newalignmentalgorithmsaredescribedinthemanuscriptby
Thompsonet.al.above,anascii/textversionofwhichisincluded
（clustalw.ms）.Thisfilelistssomeofthedetailsnotcoveredbyeither
oftheabovedocuments.
Therearebriefnotesonthefollowingtopics:
1）InstallationforVMSandUNIXandMACandPC
2）Fileinput
3）fileoutput
4）changestothealignmentalgorithms
5）minormodificationstothephylogenetictreeandbootstrappingmethods
6）summaryofthecommandlineusage.
-------------------------------------------------------------------
1）INSTALLATION（forUnix,VAX/VMS,PCandMAC）
*****IMPORTANT*****
Ifyouwishtorecompiletheprogram（orcompileitforthefirst
time;
youwillhavetodothiswithUNIXorVAX）:
firstcheckthefileCLUSTALW.Hwhichneedstobechangedifyou
movethecodefrombetweenunixandvmsmachines.Atthetop
ofthefilearefourlineswhichdefineoneofVMS,MSDOS,MACor
UNIXtobe1.AlloftheseEXCEPTonemustbecommentedout
usingenclosed/*...*/.
*******************
Unix
-----
Makefilesaresuppliedforunixmachines.Thecodewascompiledand
testedusingDecstation（Ultrix）,SUN（GnuCcompiler/gcc）,Silicon
Graphics（IRIX）andDEC/Alpha（OSF1）.Wehavenottestedthecodeonanyother
systems.Justusemakefiletomakeonmostsystems.ForSun,youneedto
havetheGnucC（gcc）compilerinstalled...usethefilemakefile.suninthis
case.Youmaketheprogramwith:
make（ormake-fmakefile.sun）
Thisproducesthefileclustalwwhichcanberunbytypingclustalwand
pressingreturn.Thehelpfileiscalledclustalw_help
VMS
----
ThereisasmallDCLcommandfile（VMSLINK.COM）tocompileandlinkthe
codeforVMSmachines（vaxoralpha）.Thisprocedurejustcompilesthe
sourcefilesandlinksusingdefaultsettings.Runitusing:
$@vmslink
ThisproducesClustalw.exewhichcanberunusingtheruncommand:
$runclustalw
Theintermediateobjectfilescanbedeletedwith:
$del*.obj;
Thereisanextensivecommandlinefacility.Tousethis,youmust
createasymboltoruntheprogram（andputthisinyourfile）.
e.g.
$clustalw:
==$$drive:
[dir.dir]clustalw
where$driveisthedriveonwhichtheexecutablefileisstored（clustalw.exe）
and[dir.dir]isthefulldirectoryspecification.NOTETHEEXTRADOLLARSIGN.
Thentheprogramcanberunusingthecommand:
$clustalw
Thehelpfileiscalledclustalw.hlp...thismustbedefinedtobe
clustalw_helpusingthecommand:
$defineclustalw_help$drive:
[dir.dir]clustalw.hlp
where$driveisthedrivenameand[dir.dir]isthenameofthe
directorywherethehelpfileisstored.
PC
__
Wesupplytwoexecutablefiles（Clustalw.exeandClwbig.exe）whichwillrun
usingMSDOS.Theywillalsorununderwindows（asaDOSapplication）
***IFyouhaveamathscoprocessor***.Ifyoudonothaveamathschip
（e.g.80387）,theprogramcanonlyberununderMSDOS.Inthelattercase,
youmusthavethefileEMU387.exeinthesamedirectoryasCLUSTALW.EXE.
Thisfileemulatesamathschipifyoudonothaveone.
WegeneratedtheseexecutablefilesusinggnucforMSDOS.
Itwillalsocompile（withabout10,000warningmessages）
usingMicrosoftCbutwehavenottesteditandthereappeartobeproblems
withtheexecutable.
Youwillneedtousea"
memoryextender"
toallowtheprogramtogetatmore
than640kbofmemory.
Clustalw.exe:
upto100sequencesofmax.length1500residues（includingGAPS）
Clwbig.exe:
upto150sequencesofmax.length2600residues（includingGAPS）
MAC
---
Thecodecomp
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