1f07984cb29634459d26d6542be0acba *DESCRIPTION
470b0d5271f48d1f85d50f49f26083f0 *NAMESPACE
d442216b326f00691c1db31afa6043cd *NEWS
4a1fcf88e8d6a8237c240b6364b3d663 *R/Coalescent.R
88a96a662a8e491bf45661466250d0a1 *R/Densi.R
db718843face57068ea5d842cccc22e2 *R/clanistic.R
e4992df0ce2eaeb1380543eed22aa769 *R/dist.p.r
afc666deca48b167d9c5ca4e9903a30e *R/distSeq.R
aa19215818ab890608d28995977b7651 *R/fitch.R
be5eb340ac24fcc83d0ac0eca6b0dc25 *R/networx.R
96b4b607b30c9e8e5bab06cb0d2a1321 *R/parsimony.R
063790a14087e919ebed48400659e21a *R/phyDat.R
c8b24767acfea5d43d4306127d3f1cf1 *R/phylo.R
b94cffafb9d7f49bfa85a2fe13ef1527 *R/sankoff.R
2b4d6884b4ee2b92e617cea76f79d3da *R/sysdata.rda
8182ad92bd5794d15c06d6f15905b5ff *R/treeManipulation.R
a55ecb8ae5ee7f0d7ac012393769ed12 *R/zzz.R
61b3722df2ead748e0db8595428412a1 *README
734b3546e92c66c4244fc7e3f34bf145 *TODO
4a92b07bcd170e85bd237e460acafa93 *data/Laurasiatherian.RData
4b269c2e640293341b9b1c04d4dd7f4e *data/chloroplast.RData
19f84425e8caaf9f605490cdff17dd81 *data/yeast.RData
b4d3fa3f40aae3a68846d1f28274e9a0 *inst/CITATION
134c26ba7b4e42189f74b4eebc7e6c63 *inst/doc/Ancestral.R
b68d79ab62b5da47d1ceda2567c31ba6 *inst/doc/Ancestral.Rnw
b429ae0fccba66a176a0666b06ecbe3f *inst/doc/Ancestral.pdf
e50cbbd6972a77a58135eea108ddd7aa *inst/doc/Trees.R
10958186df7d96a454158072e5d5d668 *inst/doc/Trees.Rnw
49d1e740c03a2c7580c2f11081e662bd *inst/doc/Trees.pdf
ccf84f185d047f947b65175bd65c3583 *inst/doc/phangorn-specials.R
49691d858c4ed96b511f0072b89da8d4 *inst/doc/phangorn-specials.Rnw
de1bc5ccf9b68bcee8c71b75aa6b86c0 *inst/doc/phangorn-specials.pdf
3009f9da02a198cb557d435cc5ad8c7f *inst/extdata/Blosum62.dat
72f496d4c6e937ffe744d25bd8891313 *inst/extdata/Dayhoff.dat
5aa357dab0e72b27023e4302bc37dbad *inst/extdata/FLU.dat
7f63f617d5d29421b0bd90ab8511feb7 *inst/extdata/HIVb.dat
29e1aa10906a86bb9bca6d9c7f98a6cb *inst/extdata/HIVw.dat
ca86e539345fa57de5c77a60308bed09 *inst/extdata/JTT.dat
fdc1176d0c0f2db3de1c9dfd83d3c070 *inst/extdata/MtZoa.dat
106715eba35efc2743ccad7923ac13ce *inst/extdata/RtREV.dat
e05f5a0ca507e4e15e7b95d1ce93b9fa *inst/extdata/VT.dat
fc090d051ce4f18b937448a254e2764e *inst/extdata/cpREV.dat
50c707c26bf9015b37670f15d5e1c14b *inst/extdata/dayhoff-dcmut.dat
6da24109959f0c7a7db50c8db78d5d42 *inst/extdata/jtt-dcmut.dat
ddc4bd45521cd72848aaf2f79b90ac6e *inst/extdata/lg.dat
917303a3df098f9137c651de0afa78fa *inst/extdata/mtArt.dat
1cd5e39670b86d32b5fe5c27dcc79648 *inst/extdata/mtREV24.dat
0ca0d0e987fcebf847a876779eddd934 *inst/extdata/mtmam.dat
87fa1533c4dfe7074237cfa2196bcbeb *inst/extdata/wag.dat
985da8b17504af26eff230a7160f208e *man/Ancestors.Rd
bda5669b71de975e1309d909c495b71f *man/Laurasiatherian.Rd
4d6fb151c28a597eadc0d4ec2c59a504 *man/NJ.Rd
e499b3bd5f3315d187531c99bd776d9f *man/SH.test.Rd
6403c950d8f9700d3fe1c847970461ef *man/allTrees.Rd
b2e1d318b90dd0affa07e2247d563f9a *man/ancestral.pml.Rd
573f2589e5925533ca28f6c5327bebae *man/as.splits.Rd
c080fc44f1f3101ea84d86b3d4932f17 *man/bab.Rd
54c70e5692cba277b3f37fc991e472b8 *man/bootstrap.pml.Rd
22ad0ef60c2edd8b3d003f170f2fa15a *man/chloroplast.Rd
00262d2601fce566e8f01a923babf8c2 *man/consensusNet.Rd
cbc985b26c68b87ab85c6a96de705da3 *man/densiTree.Rd
20f30cceced0e7188e76e70b4c947a32 *man/designTree.Rd
924c4e906042d64ac4fc4907af8c6cf1 *man/dfactorial.Rd
d9f9faa9c4048b99a1c28b76d1f73ea7 *man/dist.hamming.Rd
e7e01cc12be2fac182ff773826ad286f *man/dist.p.Rd
dbc23facc26a85fbc08711c754894cbb *man/distanceHadamard.Rd
72abceeb247f22b3da6560df0c20468a *man/getClans.Rd
f62c5014070a1478e9dade5992d31c6d *man/hadamard.Rd
9c306689d9d7cd539d8d1055b35e24a2 *man/lento.Rd
f24a38210a0e90d3241e27514a6f5b8a *man/midpoint.Rd
970c755f7ac1a0d81ca7d38bf2119a9f *man/modelTest.Rd
9734364abdb5d0122e1b4850d03b6d18 *man/nni.Rd
694fb90d75c4fff03ce2a141b1df2846 *man/parsimony.Rd
06d3770fff0d07f19393875735cfa004 *man/phangorn-package.Rd
20ab2e9ecabe1d3cae7c499b02e92824 *man/phyDat.Rd
14a7e929fbb98cc622439b4bc3117bca *man/plot.networx.Rd
2e9d65ada506013500f40c2098066d35 *man/pml.Rd
9339adbeebc944cc20d89caf8d46c544 *man/pmlCluster.Rd
8b06bdee57c510a690ea04b40bac4844 *man/pmlMix.Rd
7c78d87bd359b2097dfd05b1e6b97621 *man/pmlPart.Rd
18fb589c1c09c9a494098a6d04d3dbad *man/read.aa.Rd
4e058643bd5171e08ef7dff5a3bf9f3e *man/simSeq.Rd
9a50832f0097b8399f83d65b34937f76 *man/splitsNetwork.Rd
2614e984b5c5aa40d9364d3542172654 *man/superTree.Rd
6c36eee241785d02e58e26d735f6306b *man/treedist.Rd
64399c9fb7fb25d103c25aa925ab7a10 *man/upgma.Rd
b97649fe8b91a0632a1ded89a6f43125 *man/yeast.Rd
d2d14de06cb10e5f83eb3b7b2029b6b6 *src/Makevars
3a2422d34ab5b97b103da994f785c332 *src/dist.c
ed9b5bd9ae11ee3ca8eb9a022aec78ec *src/dist.h
1e4e33c1bb21f47865ef795a39f4ac01 *src/fitch.c
61a21fa9bd9832a65e7d62a33724dfc7 *src/fitch.h
715c1ff2c73309788efd883b2a6a15d3 *src/init.c
e704b777e8195b0e5c426096b928951d *src/ml.c
2179d0fa5e587bc128cdc716604f99c7 *src/ml.h
b5f32d1d6bee9330fdb25f9131db89cb *src/phangorn.c
29a321cd209c3a087d0c11795cd285c5 *src/phangorn.h
a4bc08d5b25bd045685c05dea98f7aed *src/sankoff.c
1175b2939bf5d8d799cec54c7e0a94da *src/sankoff.h
b68d79ab62b5da47d1ceda2567c31ba6 *vignettes/Ancestral.Rnw
9608eda76927e9438fa12a63ef8692cd *vignettes/Trees.RData
10958186df7d96a454158072e5d5d668 *vignettes/Trees.Rnw
6af5f4d4c2e93469cc19d46a97ab5d0f *vignettes/exdna.txt
49691d858c4ed96b511f0072b89da8d4 *vignettes/phangorn-specials.Rnw
8e3ab3ba583690ebd4eb944d371960f4 *vignettes/phangorn.bib
d3069d1eff9e70bed655b8962bf4ee2b *vignettes/primates.dna
