软件包：r-cran-ape（5.7-1）
GNU R package for Analyses of Phylogenetics and Evolution
This package provides 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.
其他与 r-cran-ape 有关的软件包
|
|
|
|
-
- dep: libc6 (>= 2.29)
- GNU C 语言运行库：共享库
同时作为一个虚包由这些包填实： libc6-udeb
-
- dep: libgcc-s1 (>= 3.5)
- GCC 支持库
-
- dep: liblapack3
- Library of linear algebra routines 3 - shared version
- 或者 liblapack.so.3
- 本虚包由这些包填实： libatlas3-base, liblapack3, libopenblas0-openmp, libopenblas0-pthread, libopenblas0-serial
-
- dep: libstdc++6 (>= 11)
- GNU 标准 C++ 库，第3版
-
- dep: r-api-4.0
- 本虚包由这些包填实： r-base-core
-
- dep: r-base-core (>= 4.2.2.20221110-2)
- GNU R core of statistical computation and graphics system
-
- dep: r-cran-digest
- GNU R package for 'hash digest' of R data structures
-
- dep: r-cran-lattice
- GNU R package for 'Trellis' graphics
-
- dep: r-cran-nlme
- GNU R package for (non-)linear mixed effects models
-
- dep: r-cran-rcpp (>= 0.12.0)
- GNU R package for Seamless R and C++ Integration
-
- rec: r-cran-phangorn
- GNU R package for phylogenetic analysis
-
- sug: clustalw
- global multiple nucleotide or peptide sequence alignment
-
- sug: muscle
- Multiple alignment program of protein sequences
-
- sug: phyml
- Phylogenetic estimation using Maximum Likelihood
-
- sug: r-cran-expm
- GNU R Computation of the matrix exponential and related quantities
-
- sug: r-cran-gee
- Generalized Estimation Equation Solver
-
- sug: r-cran-igraph
- GNU R network analysis and visualization
-
- sug: t-coffee
- Multiple Sequence Alignment