5f1176b9881b746b8f4050ee117a1ad0 *DESCRIPTION
45c295da94fea7cf585755e86a417cfe *NAMESPACE
b65c3883d7756a77119616b5641bc42a *R/muscle_main.R
82321ad88505df60eb3614c64516a6e3 *data/umax.rda
d3c78f2bc7683992b0dd7d0f5414a598 *inst/CITATION
03a998ff7493c512d6642670ee1295f3 *man/muscle-package.Rd
bf83d5c3d268f4d3e8090e8a8e5c6cea *man/muscle.Rd
e2eae854451fb4c133bc3808a90d3274 *man/print.muscle.Rd
86158277da13703e74ee870450f8ce10 *man/read.fasta.Rd
5a8289eb61758eeb544f11ad1fa20caa *man/umax.Rd
7d4b9f2007491812aa6297f6d7d312dd *man/write.fasta.Rd
df5c4f9f796ee5289228300714b86ce8 *src/aligngivenpath.cpp
0b2606044ed586df7d48f7d3d993c785 *src/aligngivenpathsw.cpp
985c13953f86b2ed8930c1483538ebea *src/aligntwomsas.cpp
413144a143f18da96e8fa90a2ce3bffa *src/aligntwoprofs.cpp
3e6ba5a67c540a0c3628ccde6457d250 *src/aln.cpp
870c5f5b297729aeeb5e9500126a076d *src/alpha.cpp
fd7e765f235ad1b4bf97d94e158127c7 *src/alpha.h
94df3c8d7286e6acbacdc70f6b1a4e27 *src/anchors.cpp
a87844017a80425b59fef2d55c3c7250 *src/bittraceback.cpp
920d4d9ca4cb30bf9f68178828bc6fa3 *src/blosum62.cpp
cf31b3e5a3fd4b90c552ca8a048e34cc *src/blosumla.cpp
1ab2d3eb7c9a45092557e70274ca5e5a *src/clust.cpp
0bae16486d649a5108e2ac986a3eba7c *src/clust.h
6a5bf76836a8a0a3853b524ea00a37d6 *src/cluster.cpp
89f1b8a630662233546e5c057d9cb58b *src/cluster.h
9e414d9dd3048bd5d5a4ee54142edb4b *src/clustset.h
42a14241e21eb8d5176916595683e137 *src/clustsetdf.h
bd7029d31a667da310e631bb5bf190c4 *src/clustsetmsa.h
d0c3f4820470d2f7f1caeb8ff0e6c58c *src/clwwt.cpp
c46e79bff1c5d27901e6a8fc7f80f543 *src/color.cpp
348b5f021d145de2c0b0dea576e5d9f6 *src/cons.cpp
384dd6a61b54edb934bc166a93e8b712 *src/diaglist.cpp
564af619d444b922fc7ecd3e1479fdf8 *src/diaglist.h
c56750d1cbb8969c9954523e72c47636 *src/diffobjscore.cpp
dcd1739d3f1057cffda56d5c9a4134cc *src/diffpaths.cpp
ce85603cd52c8a01630dea2942cdf622 *src/difftrees.cpp
ddcc9828384e368777db12b2c2a6ef4f *src/difftreese.cpp
07fff5a1b121c6f13173206d143e71bd *src/distcalc.cpp
a8deaa16377d4854d33f8533cc02c9ef *src/distcalc.h
acc3f7d3fe117e89efa9ae03979a876f *src/distfunc.cpp
e31d4acdc06d6ead9521be4e81734a2f *src/distfunc.h
89f04c3f928f5053744a5ef5626ed33b *src/distpwkimura.cpp
06e68e5be6e99f5ea3bd50f51efbb417 *src/domuscle.cpp
8f15cce8fffecb8df78fbad70e1d7d3e *src/dosp.cpp
845ef5345c5f15d20bf58a0b71f4c01a *src/dpregionlist.h
a6e10b44d29aa430a94ec55c861e330a *src/dpreglist.cpp
d28ea76f54fbc5046c4d17aa96af5687 *src/dpreglist.h
15226a8f7c42632937f129b34b464718 *src/drawtree.cpp
6722a8d702e8382b109f917cb6374c61 *src/edgelist.cpp
a6a63e1126fc86467bb2144f0682684a *src/edgelist.h
72ab9d5a019985926a1da914766a4a2e *src/enumopts.cpp
c2d3abaaf4ce2a4f09a6c84b026d3c42 *src/enumopts.h
96e45676530d9decef14aaf205626518 *src/enums.h
549c41222ec64cf5749c92e8504d5a94 *src/enumtostr.cpp
7c0689fcf966e302b9ade7bc4809a442 *src/estring.cpp
f3aa96d9e4d1e68e45f7ac89f6f91cfe *src/estring.h
6533676688cea2f921853a46ff0f87b0 *src/fasta.cpp
7c3f2f8fe20cc0adaa09050eabca2d9b *src/fasta2.cpp
d76cb28ce8dcd91fc6df4ae4792ecec2 *src/fastclust.cpp
38a7f80c89048a9ded39a77ef9848880 *src/fastdist.cpp
07ab017731c009ecb85ab5c8ff90711f *src/fastdistjones.cpp
84b0d32c48b68222fd24718c94292843 *src/fastdistkbit.cpp
76010e82eb2a78360e29aeee437c7c81 *src/fastdistkmer.cpp
4934cb7398e01930245b1614e91b503a *src/fastdistmafft.cpp
10dcbfdb95af33d0c0015e5c65d0bbbf *src/fastdistnuc.cpp
2298e7c963abd80c6d9fc80d940fba5b *src/fastscorepath2.cpp
ec25354a3c0aadf10372a80d02bf0cdd *src/finddiags.cpp
9c64fca6ea584066f34de6281d261d82 *src/finddiagsn.cpp
a5b7828496dd7875d6e8d5d6c0659288 *src/gapscoredimer.h
0782935566513dce4cd9c73b38344d6d *src/glbalign.cpp
3a6a650dc48d493bfd6d5004beb0a7e2 *src/glbalign352.cpp
648b992520d64077e985a934822cf4cc *src/glbaligndiag.cpp
c0e3e0a5519f45f379682f6e0eb213be *src/glbalignla.cpp
a12405f7ac3c9018baa3d064b9687ad2 *src/glbalignle.cpp
337495b55566123bdf1656ce62368547 *src/glbalignns.cpp
30a4b8dcaf56f31d71b2f1b7efef65b9 *src/glbalignsimple.cpp
a4925303eaae808d65d0dd8f08c90fc7 *src/glbalignsp.cpp
59b6cf9dcb6f6d72cdb88c2b84bb4e90 *src/glbalignspn.cpp
c9255d942be12085309a4122bd845d52 *src/glbalignss.cpp
495401a54c5a1979802337dec5bbfccc *src/glbalndimer.cpp
82800eb71e93b024fac9796a98d76023 *src/globals.cpp
25fc9feeedba31b7ae80979767b4e88f *src/globalslinux.cpp
3be218b4e79253ffd0cb2dbf76e2ff4a *src/globalsosx.cpp
e866a3ae56be464e837f4c30b775ee49 *src/globalsother.cpp
99f5f17557fff61c687785a0dd45004c *src/globalswin32.cpp
1912648ce1e428575f0d86d37ea66d76 *src/gonnet.cpp
dd586cde76b818129e5781a5186cdc43 *src/gonnet.h
d41d8cd98f00b204e9800998ecf8427e *src/gotowt.cpp
698ce441274f737f031d90fdb377ea86 *src/handle_fasta.cpp
834146cd39d57f87a5acac99fd276020 *src/henikoffweight.cpp
165748b17689b025ec07128289884670 *src/henikoffweightpb.cpp
6adc7159ecf68695affe6237c29b2ab3 *src/html.cpp
4e02a402f0fd86a731edd925152b22a6 *src/hydro.cpp
720c195991738f7572506f5b38ec6d0f *src/intmath.cpp
97ca90f7c59db662e979d9af24e0ebea *src/intmath.h
e8dbbcdd710470260b4d1c2a4dcd3003 *src/local.cpp
f19ad03cba78b2c74baede385aadbb81 *src/main.cpp
d3baea8a5a021b1ab19169962a524a8f *src/makerootmsa.cpp
08153f198c45f73ff23463aae2d42516 *src/makerootmsab.cpp
234e7e44828f38d78d44634939d1ecf4 *src/maketree.cpp
21b3fae8d877a33c515dedf1260e73df *src/mhack.cpp
2ac270068968bb0e1d53d51916d420f3 *src/mpam200.cpp
c600dcc98e3f9255f9b0815069e8aeb3 *src/msa.cpp
90e326fcd8ed33cb6a7825082a5f2cdf *src/msa.h
533d569db43e9d5f0f5706b170b65c01 *src/msa2.cpp
1546eb737efecf422b5a758e07c26e09 *src/msadist.h
e79db1b93f44f47be6b299fbd535d441 *src/msadistkimura.cpp
727b0b815951622c061afff39528d148 *src/msadistkimura.h
585b9575b84f27ba92d94de488022ce8 *src/msadistmafft.h
c8ea1054990cf994a2d8ae55ae8ef38b *src/msf.cpp
67d3f98196c53cd614c503a5716d70e5 *src/muscle.cpp
3eb3e13c9b90a140db49edcefcf1985c *src/muscle.h
b12ea66f0deb1f710719923673e03777 *src/muscleout.cpp
c83a9a4974c170411d3d8adeccf44988 *src/nucmx.cpp
2eeaa4eb772a4609e2cac808e55f1eb3 *src/nwdasimple.cpp
2b9646c8c2d510fd2c250bb367fc9251 *src/nwdasimple2.cpp
7e5d6c0538b1ab7a6f7d3d0b2a7b3a0e *src/nwdasmall.cpp
e966a47ced7509da2793307ae0897703 *src/nwrec.cpp
d538366e394a992d0a6b28cd7969f255 *src/nwsmall.cpp
a208739852ba3bb9c39755a500eecadd *src/objscore.cpp
36c42d4b872d2b31574603e3eb3c63f5 *src/objscore.h
0a6a2a3abf6182c6c87a7bdf32a0cdfb *src/objscore2.cpp
a5716d3d2585eea0a799cfb0f053e223 *src/objscoreda.cpp
f15477c56a65a26e8c7fbf0cd47576f5 *src/onexception.cpp
b64f13d39f34a9ceb3dd6e77f978be59 *src/optionsR.cpp
bb1513b101b42c0740a2cb99fc6e5ba8 *src/outweights.cpp
bb2e11ec5fd321a28ac60e6f0e30798d *src/pam200mafft.cpp
8ab4934c27b0ac0764933c5540c3169e *src/params.cpp
a2ff0cf34bcf8cdd32ab0cea129a4554 *src/params.h
5b7b9aa4cedb992128fe89ae65bcaad5 *src/phy.cpp
2f3b325e6cd88613f8690b516dfca231 *src/phy2.cpp
fe7fbcc0f385b28e5f7d91f91b6350fd *src/phy3.cpp
ad1875d0f9229b758208c1b84bf010ac *src/phy4.cpp
420592002833d144aace134a883eec7d *src/phyfromclust.cpp
a7c59446f1569d1b45e8aacc8f2c0d36 *src/phyfromfile.cpp
012c9e4ccb50d3549e22ab7ff941978f *src/physeq.cpp
69cb6fbf95f6c14111c9721c749fd0db *src/phytofile.cpp
4b835967c7d11cb8f4a2ab497346b2c7 *src/posgap.cpp
a961b24a4c58bcca186d424802a6db31 *src/ppscore.cpp
16f06c47260a72c6bff46fabe5d6a5ca *src/profdb.cpp
ff642ad7e1329224417a4a55f13e0800 *src/profile.cpp
2fe04ad7e55e6aebd868631b6383c309 *src/profile.h
d089243556113b1b04176252f7439e96 *src/profilefrommsa.cpp
af9e4e85e85888114ec0f35067fd5623 *src/progalign.cpp
ae92baa66b23b53fe6a00a37ca362663 *src/progress.cpp
082bf4390eb5e08fa8d357c29dfb5b72 *src/progressivealign.cpp
7475d16553ba7d425138ec0aeac35b3e *src/pwpath.cpp
e47d26e9277acdb577eba4b39b1091c2 *src/pwpath.h
c42b08af36b4d28debcb5fd857474f23 *src/readmx.cpp
59212463789d945efb413bd6c27b95a6 *src/realigndiffs.cpp
38f67d17ec12f774923a9cb31161efb7 *src/realigndiffse.cpp
71b6e8c84bd69ee05e202f8e85cd8791 *src/redblack.cpp
07ac77a4256633b777fdac031cad693a *src/refine.cpp
beb142f462e54ec005f885fe2be5749c *src/refinehoriz.cpp
4b81348b55415073090d5ccd873ad872 *src/refinesubfams.cpp
df8d568dbf4a54b0a7ee21eff82ffe69 *src/refinetree.cpp
082b5a3d6a2ae18e9f29f3b14ccfd4dd *src/refinetreee.cpp
2428637af84f35c33187ff987249ad05 *src/refinevert.cpp
eb5920ed210a1ce11c1c815b9d8a9648 *src/refinew.cpp
8e25fdbbf3cebda4f4299b7c57449845 *src/savebest.cpp
e0a73562f4d2bc52b914b7cae0ce5c0b *src/scoredist.cpp
c25cb5d65f249ff9801497fbdb2cf377 *src/scoregaps.cpp
15067463f1bb187dda906f91d530d9d5 *src/scorehistory.cpp
b28338e6b4235fbe581f4d8d4698aeac *src/scorehistory.h
9ea10d462c492fb4984ef0cbc3dc434a *src/scorepp.cpp
c088c9c8752b484cde06636bcbc88aa4 *src/seq.cpp
774e6235af154aa855e1e15a6db9b898 *src/seq.h
837b3da26b7af54e926200a07cef5c76 *src/seqvect.cpp
3d7db079067dcac2040e533b45cac0e7 *src/seqvect.h
508b573c920f5bbf262cbaced664d57f *src/setblosumweights.cpp
0ecde02bfdec28ee38d4cdebc6234d55 *src/setgscweights.cpp
a103c01995fa1dd098401539e9d558a6 *src/setnewhandler.cpp
8bba51b8a1c9376d126a623f522d12eb *src/spfast.cpp
56ee85df74317d7fdce048ebda45a9d7 *src/sptest.cpp
2d3d72a6790859bd3244751e49d5d020 *src/stabilize.cpp
714f828f48b1e0f1d582a6de01f463f1 *src/subfam.cpp
e579ff9136160d0a724e77b089803d7a *src/subfams.cpp
55f123361ae5ab2ed1d1abf9477a05c0 *src/svnmods.h
13f64a6fe87389d71d94fa0f0758ac6d *src/svnversion.h
b9dc7673e7c19501692d56e1bba3b5fe *src/sw.cpp
e3035061cd335a04c35ed424d1f77d99 *src/termgaps.cpp
9edcb3e8f2204f905f1cc793be274254 *src/textfile.cpp
a0b4862ba751a87fd9befa4e2807807e *src/textfile.h
9ac17bdaa5c9416296deff1428df8048 *src/threewaywt.cpp
78181de2c8742202c48155ac69663637 *src/timing.h
1ac7eccb29e6008f785c56395d70fe2a *src/tomhydro.cpp
0ad1cc4ced3d9873115f2a60219ec8d2 *src/traceback.cpp
fecbc2f3d0bd0d12cb7c70ed2a225aed *src/tracebackopt.cpp
540381fb35ee6f89a3bf9fd15e8b0a81 *src/tracebacksw.cpp
af4c1f19d0447e03dc8caa6d3a8bc82d *src/tree.h
80154f72cf47a7fbb5dca9d1ccb4e94d *src/treefrommsa.cpp
d5e650170925a31c9a854269f48c2b2e *src/types.h
25f139b301d5673703cea791722d97ab *src/typetostr.cpp
d1aa7175d47d3907092b3c701a19cc54 *src/unixio.h
7ed4470709bd066f2938cc1b1c208110 *src/upgma2.cpp
d3bf3269b80f67297be234ccbbf006ea *src/usage.cpp
439ed0767893fda3253aa32300cc6484 *src/validateids.cpp
967835b6c068bd7e8e7d95009267b051 *src/vtml2.cpp
e4bb62605316ce924e6ab2059f3a169e *src/writescorefile.cpp
