Entry: AAAlignment-class
Aliases: AAAlignment-class show,AAAlignment-method summary,AAAlignment-method
Keywords: classes
Description: "AAAlignment" result of pairwise sequence alignment.
URL: ../../../library/pairseqsim/html/AAAlignment-class.html

Entry: AAAlphabet-class
Aliases: AAAlphabet-class levels,AAAlphabet-method show,AAAlphabet-method
Keywords: classes
Description: Class "AAAlphabet" Amino Acid Alphabet
URL: ../../../library/pairseqsim/html/AAAlphabet-class.html

Entry: AASequence-class
Aliases: AASequence-class frequency,AASequence-method initialize,AASequence-method selfalign selfalign,AASequence,Submatrix-method show,AASequence-method
Keywords: classes
Description: "AASequence" Object representation of a protein Sequence
URL: ../../../library/pairseqsim/html/AASequence-class.html

Entry: AASequence
Aliases: AASequence
Keywords: misc
Description: AASequence constructor
URL: ../../../library/pairseqsim/html/AASequence.html

Entry: AASequenceList-class
Aliases: AASequenceList-class [,AASequenceList-method [[<-,AASequenceList-method [<-,AASequenceList-method
Keywords: classes
Description: Class "AASequenceList" - Container
URL: ../../../library/pairseqsim/html/AASequenceList-class.html

Entry: EPAM110
Aliases: EBLOSUM40 EPAM300 EPAM110 EBLOSUM30 EBLOSUM35 EBLOSUM45 EBLOSUM50 EBLOSUM55 EBLOSUM60 EBLOSUM62 EBLOSUM65 EBLOSUM70 EBLOSUM75 EBLOSUM80 EBLOSUM85 EBLOSUM90 EPAM10 EPAM100 EPAM110 EPAM120 EPAM130 EPAM140 EPAM150 EPAM160 EPAM170 EPAM180 EPAM190 EPAM20 EPAM200 EPAM210 EPAM220 EPAM230 EPAM240 EPAM250 EPAM260 EPAM270 EPAM280 EPAM290 EPAM30 PAM300 EPAM310 EPAM320 EPAM330 EPAM340 EPAM350 EPAM360 EPAM370 EPAM380 EPAM390 EPAM40 EPAM400 EPAM410 EPAM420 EPAM430 EPAM440 EPAM450 EPAM460 EPAM470 EPAM480 EPAM490 EPAM50 EPAM500 EPAM60 EPAM70 EPAM80 EPAM90
Keywords: datasets
Description: Amino Acid Substitution matrices
URL: ../../../library/pairseqsim/html/EPAM110.html

Entry: Submatrix-class
Aliases: Submatrix Submatrix-class show,Submatrix-method subFromEmboss,Submatrix,character-method subFromEmboss
Keywords: classes
Description: Class "Submatrix" Substitution Matrix
URL: ../../../library/pairseqsim/html/Submatrix-class.html

Entry: listdist-methods
Aliases: listdist listdist-methods listdist,list-method
Keywords: methods
Description: Compute distance matrix from a list
URL: ../../../library/pairseqsim/html/listdist-methods.html

Entry: readFasta-methods
Aliases: seqgrep infogrep readFasta readFasta-methods readFasta,AASequence-method readFasta,AASequenceList-method
Keywords: methods
Description: reader for databases in Fasta file format.
URL: ../../../library/pairseqsim/html/readFasta-methods.html

Entry: salign-methods
Aliases: salign salign-methods salign,AASequenceList,NULL-method salign,AASequenceList,AASequence-method salign,AASequence,AASequenceList-method salign,AASequence,AASequence-method
Keywords: methods
Description: Optimal pairwise alignment of two protein sequences.
URL: ../../../library/pairseqsim/html/salign-methods.html

Entry: sequlist
Aliases: sequlist
Keywords: datasets
Description: AASequenceList with 66 entries.
URL: ../../../library/pairseqsim/html/sequlist.html

Entry: testalign-methods
Aliases: testalign testalign-methods testalign,AASequence,AASequence-method
Keywords: methods
Description: Scoring of optimal alingments.
URL: ../../../library/pairseqsim/html/testalign-methods.html
