Showing 16 of total 16 results (show query)
ms609
TreeDist:Calculate and Map Distances Between Phylogenetic Trees
Implements measures of tree similarity, including information-based generalized Robinson-Foulds distances (Phylogenetic Information Distance, Clustering Information Distance, Matching Split Information Distance; Smith 2020) <doi:10.1093/bioinformatics/btaa614>; Jaccard-Robinson-Foulds distances (Bocker et al. 2013) <doi:10.1007/978-3-642-40453-5_13>, including the Nye et al. (2006) metric <doi:10.1093/bioinformatics/bti720>; the Matching Split Distance (Bogdanowicz & Giaro 2012) <doi:10.1109/TCBB.2011.48>; Maximum Agreement Subtree distances; the Kendall-Colijn (2016) distance <doi:10.1093/molbev/msw124>, and the Nearest Neighbour Interchange (NNI) distance, approximated per Li et al. (1996) <doi:10.1007/3-540-61332-3_168>. Includes tools for visualizing mappings of tree space (Smith 2022) <doi:10.1093/sysbio/syab100>, for identifying islands of trees (Silva and Wilkinson 2021) <doi:10.1093/sysbio/syab015>, for calculating the median of sets of trees, and for computing the information content of trees and splits.
Maintained by Martin R. Smith. Last updated 2 months ago.
phylogeneticstree-distancephylogenetic-treestree-distancestreescpp
32 stars 10.32 score 97 scripts 5 dependentsms609
TreeTools:Create, Modify and Analyse Phylogenetic Trees
Efficient implementations of functions for the creation, modification and analysis of phylogenetic trees. Applications include: generation of trees with specified shapes; tree rearrangement; analysis of tree shape; rooting of trees and extraction of subtrees; calculation and depiction of split support; plotting the position of rogue taxa (Klopfstein & Spasojevic 2019) <doi:10.1371/journal.pone.0212942>; calculation of ancestor-descendant relationships, of 'stemwardness' (Asher & Smith, 2022) <doi:10.1093/sysbio/syab072>, and of tree balance (Mir et al. 2013, Lemant et al. 2022) <doi:10.1016/j.mbs.2012.10.005>, <doi:10.1093/sysbio/syac027>; artificial extinction (Asher & Smith, 2022) <doi:10.1093/sysbio/syab072>; import and export of trees from Newick, Nexus (Maddison et al. 1997) <doi:10.1093/sysbio/46.4.590>, and TNT <https://www.lillo.org.ar/phylogeny/tnt/> formats; and analysis of splits and cladistic information.
Maintained by Martin R. Smith. Last updated 8 days ago.
evolutionary-biologyphylogenetic-treesphylogeneticscpp
23 stars 9.83 score 124 scripts 10 dependentsms609
Ternary:Create Ternary and Holdridge Plots
Plots ternary diagrams (simplex plots / Gibbs triangles) and Holdridge life zone plots <doi:10.1126/science.105.2727.367> using the standard graphics functions. Allows custom annotation, interpolating, contouring and scaling of plotting region. Includes a 'Shiny' user interface for point-and-click ternary plotting. An alternative to 'ggtern', which uses the 'ggplot2' family of plotting functions.
Maintained by Martin R. Smith. Last updated 5 months ago.
graphicsplottingplotting-in-rternary-plots
34 stars 9.46 score 103 scripts 5 dependentsms609
Quartet:Comparison of Phylogenetic Trees Using Quartet and Split Measures
Calculates the number of four-taxon subtrees consistent with a pair of cladograms, calculating the symmetric quartet distance of Bandelt & Dress (1986), Reconstructing the shape of a tree from observed dissimilarity data, Advances in Applied Mathematics, 7, 309-343 <doi:10.1016/0196-8858(86)90038-2>, and using the tqDist algorithm of Sand et al. (2014), tqDist: a library for computing the quartet and triplet distances between binary or general trees, Bioinformatics, 30, 2079–2080 <doi:10.1093/bioinformatics/btu157> for pairs of binary trees.
Maintained by Martin R. Smith. Last updated 9 days ago.
bioinformaticscomparisonphylogenetic-treesphylogeneticsquartetquartet-distanceresearch-tooltreecpp
14 stars 8.00 score 40 scriptsms609
TreeSearch:Phylogenetic Analysis with Discrete Character Data
Reconstruct phylogenetic trees from discrete data. Inapplicable character states are handled using the algorithm of Brazeau, Guillerme and Smith (2019) <doi:10.1093/sysbio/syy083> with the "Morphy" library, under equal or implied step weights. Contains a "shiny" user interface for interactive tree search and exploration of results, including character visualization, rogue taxon detection, tree space mapping, and cluster consensus trees (Smith 2022a, b) <doi:10.1093/sysbio/syab099>, <doi:10.1093/sysbio/syab100>. Profile Parsimony (Faith and Trueman, 2001) <doi:10.1080/10635150118627>, Successive Approximations (Farris, 1969) <doi:10.2307/2412182> and custom optimality criteria are implemented.
Maintained by Martin R. Smith. Last updated 8 days ago.
bioinformaticsmorphological-analysisphylogeneticsresearch-tooltree-searchcpp
7 stars 7.44 score 51 scripts
danlwarren
rwty:R We There Yet? Visualizing MCMC Convergence in Phylogenetics
Implements various tests, visualizations, and metrics for diagnosing convergence of MCMC chains in phylogenetics. It implements and automates many of the functions of the AWTY package in the R environment, as well as a host of other functions. Warren, Geneva, and Lanfear (2017), <doi:10.1093/molbev/msw279>.
Maintained by Dan Warren. Last updated 6 days ago.
30 stars 7.32 score 117 scriptsms609
Rogue:Identify Rogue Taxa in Sets of Phylogenetic Trees
Rogue ("wildcard") taxa are leaves with uncertain phylogenetic position. Their position may vary from tree to tree under inference methods that yield a tree set (e.g. bootstrapping, Bayesian tree searches, maximum parsimony). The presence of rogue taxa in a tree set can potentially remove all information from a consensus tree. The information content of a consensus tree - a function of its resolution and branch support values - can often be increased by removing rogue taxa. 'Rogue' provides an explicitly information-theoretic approach to rogue detection (Smith 2022) <doi:10.1093/sysbio/syab099>, and an interface to 'RogueNaRok' (Aberer et al. 2013) <doi:10.1093/sysbio/sys078>.
Maintained by Martin R. Smith. Last updated 4 months ago.
consensus-treephylogenetic-treesphylogenetics
3 stars 6.57 score 104 scripts 2 dependents
ropensci
phruta:Phylogenetic Reconstruction and Time-dating
The phruta R package is designed to simplify the basic phylogenetic pipeline. Specifically, all code is run within the same program and data from intermediate steps are saved in independent folders. Furthermore, all code is run within the same environment which increases the reproducibility of your analysis. phruta retrieves gene sequences, combines newly downloaded and local gene sequences, and performs sequence alignments.
Maintained by Cristian Roman Palacios. Last updated 9 months ago.
9 stars 4.75 score 14 scripts
joe-wayman
avotrex:A Global Dataset of Anthropogenic Extinct Birds and their Traits: Phylogeny Builder
Grafts the extinct bird species from the 'Avotrex' database (Sayol et al., in review) on to the 'BirdTree' phylogenies <https://birdtree.org>, using a set of different commands.
Maintained by Joseph Wayman. Last updated 8 months ago.
4.70 score 8 scriptsms609
CongreveLamsdell2016:Distance Metrics for Trees Generated by Congreve and Lamsdell
Includes the 100 datasets simulated by Congreve and Lamsdell (2016) <doi:10.1111/pala.12236>, and analyses of the partition and quartet distance of reconstructed trees from the generative tree, as analysed by Smith (2019) <doi:10.1098/rsbl.2018.0632>.
Maintained by Martin R. Smith. Last updated 1 years ago.
4.18 score 1 scripts
ealedo
orthGS:Orthology vs Paralogy Relationships among Glutamine Synthetase from Plants
Tools to analyze and infer orthology and paralogy relationships between glutamine synthetase proteins in seed plants.
Maintained by Elena Aledo. Last updated 4 months ago.
3.80 score 21 scripts
jsegrestin
comstab:Partitioning the Drivers of Stability of Ecological Communities
Contains the basic functions to apply the unified framework for partitioning the drivers of stability of ecological communities. Segrestin et al. (2024) <doi:10.1111/geb.13828>.
Maintained by Jules Segrestin. Last updated 8 months ago.
6 stars 3.78 scorems609
TBRDist:Rearrangement Distances Between Unrooted Phylogenetic Trees
Fast calculation of the Subtree Prune and Regraft (SPR), Tree Bisection and Reconnection (TBR) and Replug distances between unrooted trees, using the algorithms of Whidden and Matsen (2017) <arxiv:1511.07529>.
Maintained by Martin R. Smith. Last updated 4 years ago.
phylogeneticstree-distancedistance-calculationphylogenetic-treescpp
3.70 score
therfrog
shinyNORRRM:The Ultimate Igneous Norm
The computer program is an efficient igneous norm algorithm and rock classification system written in R but run as shiny app.
Maintained by Reneé González-Guzmán. Last updated 2 years ago.
3 stars 3.18 score 3 scriptsms609
TotalCopheneticIndex:Quantify the Balance of Phylogenetic Trees
Measures the degree of balance for a given phylogenetic tree by calculating the Total Cophenetic Index. Reference: A. Mir, F. Rossello, L. A. Rotger (2013). A new balance index for phylogenetic trees. Math. Biosci. 241, 125-136 <doi:10.1016/j.mbs.2012.10.005>.
Maintained by Martin R. Smith. Last updated 4 years ago.
1.70 score 3 scripts
cran
bexy:Visualize and Parse the Output of 'BeXY'
Provides functions for summarizing and plotting the output of the command-line tool 'BeXY' (<https://bitbucket.org/wegmannlab/bexy>), a tool that performs Bayesian inference of sex chromosome karyotypes and sex-linked scaffolds from low-depth sequencing data.
Maintained by Madleina Caduff. Last updated 7 months ago.
1.00 score