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emmanuelparadis
ape:Analyses of Phylogenetics and Evolution
Functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, ancestral character analyses, analyses of diversification and macroevolution, computing distances from DNA sequences, reading and writing nucleotide sequences as well as importing from BioConductor, and several tools such as Mantel's test, generalized skyline plots, graphical exploration of phylogenetic data (alex, trex, kronoviz), estimation of absolute evolutionary rates and clock-like trees using mean path lengths and penalized likelihood, dating trees with non-contemporaneous sequences, translating DNA into AA sequences, and assessing sequence alignments. Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and triangle methods, and several methods handling incomplete distance matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some functions call external applications (PhyML, Clustal, T-Coffee, Muscle) whose results are returned into R.
Maintained by Emmanuel Paradis. Last updated 12 hours ago.
64 stars 15.83 score 13k scripts 599 dependents
larssnip
microseq:Basic Biological Sequence Handling
Basic functions for microbial sequence data analysis. The idea is to use generic R data structures as much as possible, making R data wrangling possible also for sequence data.
Maintained by Lars Snipen. Last updated 10 months ago.
3 stars 5.46 score 54 scripts 3 dependents
bioc
muscle:Multiple Sequence Alignment with MUSCLE
MUSCLE performs multiple sequence alignments of nucleotide or amino acid sequences.
Maintained by Alex T. Kalinka. Last updated 5 months ago.
multiplesequencealignmentalignmentsequencinggeneticssequencematchingdataimportcpp
5.21 score 81 scripts
mhahsler
rMSA:Interface for Popular Multiple Sequence Alignment Tools
Seamlessly interfaces the Multiple Sequence Alignment software packages ClustalW, MAFFT, MUSCLE and Kalign (downloaded separately) and provides support to calcualte distances between sequences. This work was partially supported by grant no. R21HG005912 from the National Human Genome Research Institute.
Maintained by Michael Hahsler. Last updated 10 months ago.
geneticssequencinginfrastructurealignmentbioinformaticssequence-alignment
12 stars 3.78 score 7 scripts