a95bb2db4b6503e7dec321cef6bd29c0 *DESCRIPTION
5fc2790cc77060358b14b1de3fcfc5e1 *NAMESPACE
58ab085f59179c96b34b59b63228a12e *NEWS
545fc6af9a418883b377eba5c3ce0187 *R/00datacache.R
9a2f0df9ec1475717f8e6ba158487124 *R/AlignedXStringSet-class.R
50089ae1c23fea89a04deadd6051e277 *R/InDel-class.R
8d6a5f7fd8544df6da8103fd6b48b8f4 *R/PairwiseAlignments-class.R
e399018a00b83cf1b21cae139e551bde *R/PairwiseAlignments-io.R
9ec3b4a2c4d1fc8d978a8f0e83c651a9 *R/PairwiseAlignmentsSingleSubject-class.R
efda21c369eb1c5d93b71e46ae963dad *R/align-utils.R
635003cc414b413f8787d102ed1054ff *R/pairwiseAlignment.R
7e3be796fb9321e16d73db0d0558523f *R/pid.R
c2289a66234fadbfde4e8213836a9199 *R/stringDist.R
33bdad994152fd0383c42bdb4358fcf8 *R/substitution_matrices.R
d5a6dd427d7da1ba46cf13988e04681b *R/utils.R
d1949347bf0b2794ed9f1e10c5b899d5 *R/zzz.R
901bb34e8abf8ef39674cfd51b230fa1 *README.md
6d74d54ec4897bd233e14ea98a0fefb5 *TODO
9a7061c026561e4521c82b9192dc29d3 *build/vignette.rds
fb21544885b0d8e223dc707a19f703a6 *data/BLOSUM100.rda
370ae409745a34652b50f6c0992a7c36 *data/BLOSUM45.rda
ff21fdf7ae6c26d41265485e06678c47 *data/BLOSUM50.rda
938f1640bbcee65ce83726127c8efa8f *data/BLOSUM62.rda
ec70a69370ee7b924a1521bd22a0b92a *data/BLOSUM80.rda
b85025df056de88ad4e0ec260b4fbd3e *data/PAM120.rda
d790bbcef52f77bdbac03ca4fe317a0d *data/PAM250.rda
5ab6a6fb04f2bb2011c96abdea970b87 *data/PAM30.rda
d234baa0914f6233478aa0687fdbe10c *data/PAM40.rda
8533b9535b841e231b9babd78d584885 *data/PAM70.rda
d1f902614de1a9eba90d8387690c2688 *data/phiX174Phage.rda
ea5bd4d16695006aab9061c351649bb6 *data/srPhiX174.rda
49f9f04818cacff1647256d3c126a0d4 *inst/doc/PairwiseAlignments.R
046214dd7deab89e4bfdd4f869321570 *inst/doc/PairwiseAlignments.Rnw
232d64269a3724e52a3b0d20fd785f88 *inst/doc/PairwiseAlignments.pdf
81024370010e243c14bd882b4cb9a727 *inst/unitTests/test_pairwiseAlignment.R
98789bd53d4b669cde3c339e62df840e *man/AlignedXStringSet-class.Rd
2135c4418562f779ff5152e1137e5e2f *man/InDel-class.Rd
64045a5f8804f73c7a225002339ef867 *man/PairwiseAlignments-class.Rd
8a6bbbf84a178384a4953649056b5875 *man/PairwiseAlignments-io.Rd
72490bf4f3c19afbea4ca1fb3eb7673a *man/align-utils.Rd
a76a8cf9197230fcff3136b1799fcbdd *man/pairwiseAlignment.Rd
fcf02860d3d8d4183a53c17c4fc7e8a8 *man/phiX174Phage.Rd
8616b90f9f5504b8bc7909394f4fb96f *man/pid.Rd
7245465ea2a25c8caa02098e3f3a7d86 *man/predefined_scoring_matrices.Rd
7eeaab428152fd7ae20fc57124e446d5 *man/stringDist.Rd
dd9384d71e8e9b9fc408aa111042ff6a *man/substitution_matrices.Rd
f1f4685a8f0afb74e19c344a86d86b22 *src/Biostrings_stubs.c
b0447144238dce005a1fa8a625d1563c *src/IRanges_stubs.c
ea7d90a65c6c7082f0a7ef701493b36f *src/R_init_pairwiseAlignment.c
bab0b4b09cf160fa0109ae25fbb471ef *src/S4Vectors_stubs.c
07fbf9ef7d1a296302e6de26aa821a44 *src/XVector_stubs.c
fcd576c561b473a0ec7fdb00a33fd2f0 *src/align_pairwiseAlignment.c
4f3e86828fd5228aed9bc74f7b8cfc9c *src/align_utils.c
006986aa6666b4217b1f120e8c4020d6 *src/pwalign.h
83becba95d34c37f991d61ce435904a3 *tests/run_unitTests.R
046214dd7deab89e4bfdd4f869321570 *vignettes/PairwiseAlignments.Rnw
