# FreeBSD Manual Pages

- fasta(1)
- scan a protein or DNA sequence library for similar sequences tfasta - compare a protein sequence to a DNA sequence library, translating the DNA sequence library `on-the-fly'. lfasta - compare two protein or DNA sequences for local similarity and show the local sequence alignments plfasta - compare two sequences for local similarity and plot the local sequence alignments
- lalign(1)
- compare two protein or DNA sequences for local similarity and show the local sequence alignments plalign,flalign - compare two sequences for local similarity and plot the local sequence alignments
- pcgehd2(l), PCGEHD2(l)
- reduce a complex general distributed matrix sub( A ) to upper Hessenberg form H by an unitary similarity transformation
- pcgehrd(l), PCGEHRD(l)
- reduce a complex general distributed matrix sub( A ) to upper Hessenberg form H by an unitary similarity transformation
- pchetd2(l), PCHETD2(l)
- reduce a complex Hermitian matrix sub( A ) to Hermitian tridiagonal form T by an unitary similarity transformation
- pchetrd(l), PCHETRD(l)
- reduce a complex Hermitian matrix sub( A ) to Hermitian tridiagonal form T by an unitary similarity transformation
- pclatrd(l), PCLATRD(l)
- reduce NB rows and columns of a complex Hermitian distributed matrix sub( A ) = A(IA:IA+N-1,JA:JA+N-1) to complex tridiagonal form by an unitary similarity transformation Q' * sub( A ) * Q, and returns the matrices V and W which are needed to apply the transformation to the unreduced part of sub( A )
- pdgehd2(l), PDGEHD2(l)
- reduce a real general distributed matrix sub( A ) to upper Hessenberg form H by an orthogonal similarity transforma- tion
- pdgehrd(l), PDGEHRD(l)
- reduce a real general distributed matrix sub( A ) to upper Hessenberg form H by an orthogonal similarity transforma- tion
- pdlatrd(l), PDLATRD(l)
- reduce NB rows and columns of a real symmetric distributed matrix sub( A ) = A(IA:IA+N-1,JA:JA+N-1) to symmetric tridiagonal form by an orthogonal similarity transformation Q' * sub( A ) * Q,
- pdsytd2(l), PDSYTD2(l)
- reduce a real symmetric matrix sub( A ) to symmetric tridiagonal form T by an orthogonal similarity transformation
- pdsytrd(l), PDSYTRD(l)
- reduce a real symmetric matrix sub( A ) to symmetric tridiagonal form T by an orthogonal similarity transformation
- prdf(1)
- test a protein sequence similarity for significance
- prss(1)
- test a protein sequence similarity for significance
- psgehd2(l), PSGEHD2(l)
- reduce a real general distributed matrix sub( A ) to upper Hessenberg form H by an orthogonal similarity transforma- tion
- psgehrd(l), PSGEHRD(l)
- pslatrd(l), PSLATRD(l)
- reduce NB rows and columns of a real symmetric distributed matrix sub( A ) = A(IA:IA+N-1,JA:JA+N-1) to symmetric tridiagonal form by an orthogonal similarity transformation Q' * sub( A ) * Q,
- pssytd2(l), PSSYTD2(l)
- reduce a real symmetric matrix sub( A ) to symmetric tridiagonal form T by an orthogonal similarity transformation
- pssytrd(l), PSSYTRD(l)
- pzgehd2(l), PZGEHD2(l)
- reduce a complex general distributed matrix sub( A ) to upper Hessenberg form H by an unitary similarity transformation
- pzgehrd(l), PZGEHRD(l)
- pzhetd2(l), PZHETD2(l)
- reduce a complex Hermitian matrix sub( A ) to Hermitian tridiagonal form T by an unitary similarity transformation
- pzhetrd(l), PZHETRD(l)
- pzlatrd(l), PZLATRD(l)
- reduce NB rows and columns of a complex Hermitian distributed matrix sub( A ) = A(IA:IA+N-1,JA:JA+N-1) to complex tridiagonal form by an unitary similarity transformation Q' * sub( A ) * Q, and returns the matrices V and W which are needed to apply the transformation to the unreduced part of sub( A )
- Bio::Annotation::Target(3)
- Provides an object which represents a target (ie, a similarity hit) from one object to something in another database
- Bio::Search::HSP::HSPI(3)
- Interface for a High Scoring Pair in a similarity search result
- Bio::Search::Hit::HitI(3)
- Interface for a hit in a similarity search result
- Bio::SeqFeature::Similarity(3)
- A sequence feature based on similarity
- Bio::SeqFeature::SimilarityPair(3)
- Sequence feature based on the similarity of two sequences
- Plucene::Search::Similarity(3)
- the score of a query
- String::Similarity(3)
- calculate the similarity of two strings
- Text::Similarity(3)
- Measure the pair-wise Similarity of Files or Strings
- Text::Similarity::Overlaps(3)
- Score the Overlaps Found Between Two Strings Based on Literal Text Matching
- WordNet::Similarity(3)
- Perl modules for computing measures of semantic relatedness
- WordNet::Similarity::DepthFinder(3)
- methods to find the depth of synsets in WordNet taxonomies
- WordNet::Similarity::FrequencyCounter(3)
- Support functions for frequency counting programs used to estimate the information content of concepts
- WordNet::Similarity::GlossFinder(3)
- module to implement gloss finding methods for WordNet::Similarity measures of semantic relatedness (specifically, lesk and vector)
- WordNet::Similarity::ICFinder(3)
- a module for finding the information content of concepts in WordNet
- WordNet::Similarity::PathFinder(3)
- module to implement path finding methods (by node counting) for WordNet::Similarity measures of semantic relatedness
- WordNet::Similarity::hso(3)
- Perl module for computing semantic relatedness of word senses using the method described by Hirst and St-Onge (1998)
- WordNet::Similarity::jcn(3)
- Perl module for computing semantic relatedness of word senses according to the method described by Jiang and Conrath (1997)
- WordNet::Similarity::lch(3)
- Perl module for computing semantic relatedness of word senses using the method described by Leacock and Chodorow (1998)
- WordNet::Similarity::lesk(3)
- Perl module for computing semantic relatedness of word senses using gloss overlaps as described by Banerjee and Pedersen (2002) -- a method that adapts the Lesk approach to WordNet
- WordNet::Similarity::lin(3)
- Perl module for computing semantic relatedness of word senses using the information content based measure described by Lin (1998)
- WordNet::Similarity::path(3)
- Perl module for computing semantic relatedness of word senses by counting nodes in the noun and verb WordNet 'is-a' hierarchies
- WordNet::Similarity::random(3)
- Perl module for computing semantic relatedness of word senses using a random measure
- WordNet::Similarity::res(3)
- Perl module for computing semantic relatedness of word senses using an information content based measure described by Resnik (1995)
- WordNet::Similarity::vector(3)
- Perl module for computing semantic relatedness of word senses using second order co-occurrence vectors of glosses of the word senses
- WordNet::Similarity::vector_pairs(3)
- module for computing semantic relatedness of word senses using second order co-occurrence vectors of glosses of the word senses
- WordNet::Similarity::wup(3)
- Perl module for computing semantic relatedness of word senses using the edge counting method of the of Wu & Palmer (1994)
- WordNet::vectorFile(3)
- Provides access to the word vectors database (used by the vector and vector_pairs WordNet::Similarity measures)
- similarity.pl(1)
- Command line interface to WordNet::Similarity
- similarity_server.pl(1)
- [Web] The backend WordNet::Similarity server for the Web Interface
- text_similarity.pl(1), text_simlarity.pl(1)
- Measure the pair-wise similarity between files or strings