Major changes to PhyKIT are summarized here.
+2.0.0: +Codebase overhaul to make PhyKIT more mem efficient and faster. For example, using list comprehension when appropriate.
1.21.0: The partition file outputted from the create_concat function has been updated to the following format: - column 1: alignment name diff --git a/searchindex.js b/searchindex.js index 2f83abe..9d47f1f 100644 --- a/searchindex.js +++ b/searchindex.js @@ -1 +1 @@ -Search.setIndex({"alltitles": {"1. Summarizing information content": [[5, "summarizing-information-content"]], "2. Evaluating gene-gene covariation": [[5, "evaluating-gene-gene-covariation"]], "3. Identifying signatures of rapid radiations": [[5, "identifying-signatures-of-rapid-radiations"]], "4. Evaluating the accuracy of a multiple sequence alignment": [[5, "evaluating-the-accuracy-of-a-multiple-sequence-alignment"]], "About": [[0, "about"]], "Alignment length": [[5, "alignment-length"], [6, "alignment-length"]], "Alignment length no gaps": [[6, "alignment-length-no-gaps"]], "Alignment recoding": [[6, "alignment-recoding"]], "Alignment- and tree-based functions": [[6, "alignment-and-tree-based-functions"]], "Alignment-based functions": [[6, "alignment-based-functions"]], "Bipartition support statistics": [[5, "bipartition-support-statistics"], [6, "bipartition-support-statistics"]], "Branch length multiplier": [[6, "branch-length-multiplier"]], "Calling functions": [[6, "calling-functions"]], "Change log": [[1, "change-log"]], "Collapse bipartitions": [[6, "collapse-bipartitions"]], "Column score": [[6, "column-score"]], "Command line interfaces": [[6, "command-line-interfaces"]], "Compositional bias per site": [[6, "compositional-bias-per-site"]], "Covarying evolutionary rates": [[6, "covarying-evolutionary-rates"]], "Create concatenation matrix": [[6, "create-concatenation-matrix"]], "Degree of violation of the molecular clock": [[6, "degree-of-violation-of-the-molecular-clock"]], "Evolutionary Rate per Site": [[6, "evolutionary-rate-per-site"]], "Evolutionary rate": [[6, "evolutionary-rate"]], "FAQ": [[2, "faq"]], "Faidx": [[6, "faidx"]], "Function aliases": [[6, "function-aliases"]], "General usage": [[6, "general-usage"]], "Guanine-cytosine (GC) content": [[6, "guanine-cytosine-gc-content"]], "Hidden paralogy check": [[6, "hidden-paralogy-check"]], "Internal branch statistics": [[6, "internal-branch-statistics"]], "Internode labeler": [[6, "internode-labeler"]], "Last common ancestor subtree": [[6, "last-common-ancestor-subtree"]], "Long branch score": [[5, "long-branch-score"], [6, "long-branch-score"]], "Monophyly check": [[6, "monophyly-check"]], "More Team Members": [[0, "more-team-members"]], "Nearest neighbor interchange": [[6, "nearest-neighbor-interchange"]], "Other software": [[4, "other-software"]], "Pairwise identity": [[6, "pairwise-identity"]], "Parsimony informative sites": [[5, "parsimony-informative-sites"], [6, "parsimony-informative-sites"]], "Patristic distances": [[6, "patristic-distances"]], "Polytomy testing": [[6, "polytomy-testing"]], "Print tree": [[6, "print-tree"]], "Protein-to-nucleotide alignment": [[6, "protein-to-nucleotide-alignment"]], "Prune tree": [[6, "prune-tree"]], "Quick Start": [[3, "quick-start"]], "Relative composition variability": [[6, "relative-composition-variability"]], "Relative composition variability, taxon": [[6, "relative-composition-variability-taxon"]], "Rename FASTA entries": [[6, "rename-fasta-entries"]], "Rename tree tips": [[6, "rename-tree-tips"]], "Robinson-Foulds distance": [[6, "robinson-foulds-distance"]], "Root tree": [[6, "root-tree"]], "Saturation": [[5, "saturation"], [6, "saturation"]], "Spurious homolog identification": [[6, "spurious-homolog-identification"]], "Step 0: Generate query alignments": [[5, "step-0-generate-query-alignments"]], "Step 0: Prepare data": [[5, "step-0-prepare-data"], [5, "id16"]], "Step 1: Conduct polytomy test": [[5, "step-1-conduct-polytomy-test"]], "Step 1: Estimate gene tree branch lengths": [[5, "step-1-estimate-gene-tree-branch-lengths"]], "Step 1: Score each alignment": [[5, "step-1-score-each-alignment"]], "Step 2: Root constrain trees": [[5, "step-2-root-constrain-trees"]], "Step 3: Evaluate gene-gene covariation": [[5, "step-3-evaluate-gene-gene-covariation"]], "Sum-of-pairs score": [[6, "sum-of-pairs-score"]], "Terminal branch statistics": [[6, "terminal-branch-statistics"]], "The Developers": [[0, "the-developers"]], "Tip labels": [[6, "tip-labels"]], "Tip-to-tip distance": [[6, "tip-to-tip-distance"]], "Tip-to-tip node distance": [[6, "tip-to-tip-node-distance"]], "Total tree length": [[6, "total-tree-length"]], "Tree-based functions": [[6, "tree-based-functions"]], "Treeness": [[6, "treeness"]], "Treeness divided by relative composition variability": [[5, "treeness-divided-by-relative-composition-variability"]], "Treeness over RCV": [[6, "treeness-over-rcv"]], "Tutorials": [[5, "tutorials"]], "Usage": [[6, "usage"]], "Variable sites": [[5, "variable-sites"], [6, "variable-sites"]]}, "docnames": ["about/index", "change_log/index", "frequently_asked_questions/index", "index", "other_software/index", "tutorials/index", "usage/index"], "envversion": {"sphinx": 61, "sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2}, "filenames": ["about/index.rst", "change_log/index.rst", "frequently_asked_questions/index.rst", "index.rst", "other_software/index.rst", "tutorials/index.rst", "usage/index.rst"], "indexentries": {}, "objects": {}, 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