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The AAindex1 section of the Amino Acid Index Database is a collection of published indices together with the result of cluster analysis using the correlation coefficient as the distance between two indices. This section currently contains 494 indices. Another important feature of amino acids that can be represented numerically is the similarity between amino acids. Thus, a similarity matrix, also called a mutation matrix, is a set of 210 numerical values, 20 diagonal and 20x19\/2 off-diagonal elements, used for sequence alignments and similarity searches. The AAindex2 section of the Amino Acid Index Database is a collection of published amino acid mutation matrices together with the result of cluster analysis. 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The usage of other programs and scripts can be found in CD-HIT user's guide."},{"categoryid":353,"description":"Scalable multiple alignment of protein sequences","firstseen":"2011-09-26T14:35:31.392681","maintainer":"sci-biology@gentoo.org","maintainername":"Gentoo Biology Project","name":"clustal-omega","packageid":57986},{"categoryid":353,"description":"General purpose multiple alignment program for DNA and proteins","firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci-biology@gentoo.org","maintainername":"Gentoo Biology Project","name":"clustalw","packageid":52977},{"categoryid":353,"description":"An MPI implemention of the ClustalW general purpose multiple alignment algorithm","firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci-biology@gentoo.org","maintainername":"Gentoo Biology Project","name":"clustalw-mpi","packageid":43775},{"categoryid":353,"description":"Codon usage tables calculated from GenBank","firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci-biology@gentoo.org","maintainername":"Gentoo Biology Project","name":"cutg","packageid":46991,"summary":"Codon usage tables maintained at the Kazusa DNA Research Institute. 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It is maintained by New England Biolabs. It contains published and unpublished references, recognition and cleavage sites, isoschizomers, commercial availability, methylation sensitivity, crystal and sequence data. DNA methyltransferases, homing endonucleases, nicking enzymes, specificity subunits and control proteins are also included. More recently, putative DNA methyltransferases and restriction enzymes, as predicted from analysis of genomic sequences, are also listed."},{"categoryid":353,"description":"Automated de novo identification of repeat families from genomic sequences","firstseen":"2011-02-03T14:39:13.740633","maintainer":"sci-biology@gentoo.org","maintainername":"Gentoo Biology Project","name":"recon","packageid":56795},{"categoryid":353,"description":"Generates 2D displays of RNA\/DNA secondary structures with tertiary interactions","firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci-biology@gentoo.org","maintainername":"Gentoo Biology Project","name":"rnaview","packageid":49285,"summary":"The RNAView program generates 2-dimensional displays of RNA\/DNA secondary structures with tertiary interactions. RNAView automatically identifies and classifies the types of base pairs that are formed in nucleic acid structures, fully implementing Leontis and Westhof's (RNA (2001) 7, 499-512), convention for edge-to-edge hydrogen bonding interactions."},{"categoryid":353,"description":"Utilities for analysing and manipulating the SAM\/BAM alignment formats","firstseen":"2010-12-22T14:41:05.491029","maintainer":"sci-biology@gentoo.org","maintainername":"Gentoo Biology Project","name":"samtools","packageid":56631},{"categoryid":353,"description":"A graphical multiple sequence alignment editor","firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci-biology@gentoo.org","maintainername":"Gentoo Biology Project","name":"seaview","packageid":54725,"summary":"SeaView is a graphical multiple sequence alignment editor developped by Manolo Gouy. SeaView is able to read and write various alignment formats (NEXUS, MSF, CLUSTAL, FASTA, PHYLIP, MASE). It allows to manually edit the alignment, and also to run DOT-PLOT or CLUSTALW programs to locally improve the alignment."},{"categoryid":353,"description":"C++ Sequence Analysis Library","firstseen":"2013-03-14T14:36:03.414471","maintainer":"sci-biology@gentoo.org","maintainername":"Gentoo Biology Project","name":"seqan","packageid":60538},{"categoryid":353,"description":"A rewrite and improvement upon sim4, a DNA-mRNA aligner","firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci-biology@gentoo.org","maintainername":"Gentoo Biology Project","name":"sibsim4","packageid":49161},{"categoryid":353,"description":"A program to align cDNA and genomic DNA","firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci-biology@gentoo.org","maintainername":"Gentoo Biology Project","name":"sim4","packageid":51727,"summary":"sim4 is a similarity-based tool for aligning an expressed DNA sequence (EST, cDNA, mRNA) with a genomic sequence for the gene. It also detects end matches when the two input sequences overlap at one end (i.e., the start of one sequence overlaps the end of the other).sim4 employs a blast-based technique to first determine the basic matching blocks representing the \"exon cores\". In this first stage, it detects all possible exact matches of W-mers (i.e., DNA words of size W) between the two sequences and extends them to maximal scoring gap-free segments. In the second stage, the exon cores are extended into the adjacent as-yet-unmatched fragments using greedy alignment algorithms, and heuristics are used to favor configurations that conform to the splice-site recognition signals (GT-AG, CT-AC). If necessary, the process is repeated with less stringent parameters on the unmatched fragments."},{"categoryid":353,"description":"Protein secondary structure assignment from atomic coordinates","firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci-biology@gentoo.org","maintainername":"Gentoo Biology Project","name":"stride","packageid":51967},{"categoryid":353,"description":"A multiple sequence alignment package","firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci-biology@gentoo.org","maintainername":"Gentoo Biology Project","name":"t-coffee","packageid":49483,"summary":"T-Coffee is a multiple sequence alignment package. Given a set of sequences (Proteins or DNA), T-Coffee generates a multiple sequence alignment. Version 2.00 and higher can mix sequences and structures. T-Coffee allows the combination of a collection of multiple\/pairwise, global or local alignments into a single model. It also allows to estimate the level of consistency of each position within the new alignment with the rest of the alignments."},{"categoryid":353,"description":"Maximum likelihood analysis for nucleotide, amino acid, and two-state data","firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci-biology@gentoo.org","maintainername":"Gentoo Biology Project","name":"tree-puzzle","packageid":46128,"summary":"TREE-PUZZLE is a computer program to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood. It implements a fast tree search algorithm, quartet puzzling, that allows analysis of large data sets and automatically assigns estimations of support to each internal branch. TREE-PUZZLE also computes pairwise maximum likelihood distances as well as branch lengths for user specified trees. Branch lengths can be calculated under the clock-assumption. In addition, TREE-PUZZLE offers a novel method, likelihood mapping, to investigate the support of a hypothesized internal branch without computing an overall tree and to visualize the phylogenetic content of a sequence alignment. TREE-PUZZLE also conducts a number of statistical tests on the data set (chi-square test for homogeneity of base composition, likelihood ratio clock test, Kishino-Hasegawa test). The models of substitution provided by TREE-PUZZLE are TN, HKY, F84, SH for nucleotides, Dayhoff, JTT, mtREV24, VT, WAG, BLOSUM 62 for amino acids, and F81 for two-state data. Rate heterogeneity is modeled by a discrete Gamma distribution and by allowing invariable sites. The corresponding parameters can be inferred from the data set."},{"categoryid":353,"description":"A phylogenetic tree viewer","firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci-biology@gentoo.org","maintainername":"Gentoo Biology Project","name":"treeviewx","packageid":53311,"summary":"TreeView X is a program for displaying phylogenetic trees on Linux and UNIX platforms. It can read and display NEXUS and Newick format tree files (such as those output by PAUP*, ClustalX, TREE-PUZZLE, and other programs)."},{"categoryid":353,"description":"Tandem Repeats Finder","firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci-biology@gentoo.org","maintainername":"Gentoo Biology Project","name":"trf","packageid":52025},{"categoryid":353,"description":"tRNA detection in large-scale genome sequences","firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci-biology@gentoo.org","maintainername":"Gentoo Biology Project","name":"trnascan-se","packageid":49297,"summary":"tRNAscan-SE detects ~99% of eukaryotic nuclear or prokaryotic tRNA genes, with a false positive rate of less than one per 15 gigabases, and with a search speed of about 30 kb\/second. It was implemented for large-scale human genome sequence analysis, but is applicable to other DNAs as well."},{"categoryid":353,"description":"Fast, accurate chimera detection","firstseen":"2012-08-15T14:43:37.194721","maintainer":"sci-biology@gentoo.org","maintainername":"Gentoo Biology Project","name":"uchime","packageid":59697,"summary":"UCHIME is a new algorithm for detecting chimeric sequences. It was developed in collaboration with Brian Haas, Jose Carlos Clemente, Chris Quince and Rob Knight. Chimeras are commonly created during DNA sample amplification by PCR, especially in community sequencing experiments using single regions such as the 16S rRNA gene in bacteria or the fungal ITS region. UCHIME can detect chimeras using a reference database or de novo using abundance information on the assumption that chimeras are less abundant than their parents because they must have undergone fewer rounds of amplification."},{"categoryid":353,"description":"The UCSC genome browser suite, also known as Jim Kent's library and GoldenPath","firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci-biology@gentoo.org","maintainername":"Gentoo Biology Project","name":"ucsc-genome-browser","packageid":53877},{"categoryid":353,"description":"Unified Nucleic Acid Folding and hybridization package","firstseen":"2011-01-14T14:42:30.477129","maintainer":"sci-biology@gentoo.org","maintainername":"Gentoo Biology Project","name":"unafold","packageid":56702},{"categoryid":353,"description":"update_blastdb.pl for local blast db maintainance","firstseen":"2014-05-14T13:37:36.083422","maintainer":"sci-biology@gentoo.org","maintainername":"Gentoo Biology Project","name":"update-blastdb","packageid":62199},{"categoryid":353,"description":"Tools for working with VCF (Variant Call Format) files","firstseen":"2011-10-03T14:35:06.100551","maintainer":"sci-biology@gentoo.org","maintainername":"Gentoo Biology Project","name":"vcftools","packageid":58004},{"categoryid":353,"description":"A sequence assembler for very short reads","firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci-biology@gentoo.org","maintainername":"Gentoo Biology Project","name":"velvet","packageid":49259},{"categoryid":353,"description":"Intelligent algorithms for DNA searches","firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci-biology@gentoo.org","maintainername":"Gentoo Biology Project","name":"wise","packageid":55024},{"categoryid":353,"description":"Genomic similarity search with multiple transition constrained spaced seeds","firstseen":"2010-06-18T14:37:58.731517","maintainer":"sci-biology@gentoo.org","maintainername":"Gentoo Biology Project","name":"yass","packageid":55912}]}