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generalized-pd

https://github.com/sriram98v/generalized-pd

Science Score: 44.0%

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Last synced: 10 months ago · JSON representation ·

Repository

Basic Info
  • Host: GitHub
  • Owner: sriram98v
  • License: mit
  • Language: Rust
  • Default Branch: main
  • Size: 79.1 KB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 1
Created almost 2 years ago · Last pushed over 1 year ago
Metadata Files
Readme License Citation

README.md

Generalized Phylogenetic Diversity

This repository contains a rust crate to compute the PD statistics of a phylogenetic tree

Installation

To install you must first have cargo and rustup installed: bash curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh

After installing the above command you can run the following to install genpd: bash cargo install --git=https://github.com/sriram98v/Generalized-PD

Alternatively, you can install seq_class by cloning this repository and building it locally: bash git clone https://github.com/sriram98v/Generalized-PD cd Generalized-PD cargo install --path=./

Usage

Finding the min and max normalized PD for fixed taxa set

To compute the minimum PD, please create a single file with the extension .tre containing the tree in Newick format. The run the following command to compute the Minimum PD: bash genpd PD min -f <PATH TO .TRE FILE> -n <NUM_TAXA>

Please refer the help page for details on how to use other path functions using: bash genpd PD min -h

for max replace min with max in the above commands. To compute min/max PD for all values of k use the all_min/all_max command.

Finding the min and max generalized PD

To compute the minimum Generalized PD, please create a single file with the extension .tre containing the tree in Newick format. The run the following command to compute the Minimum Generalized PD: bash genpd gen min -f <PATH TO .TRE FILE>

Please refer the help page for details on how to use other path functions using: bash genpd gen min -h

for max replace min with max in the above commands

Owner

  • Login: sriram98v
  • Kind: user

Citation (CITATION.cff) 

# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: GenPD
message: >-
  If you use this software, please cite it using the
  metadata from this file.
type: software
authors:
  - given-names: Sriram
    family-names: Vijendran
    email: vijendran.sriram@gmail.com
    orcid: 'https://orcid.org/0000-0002-8417-3675'
    affiliation: Iowa State University
repository-code: 'https://github.com/sriram98v/Generalized-PD'
url: 'https://github.com/sriram98v/Generalized-PD'
license: MIT

GitHub Events

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Dependencies

Cargo.lock cargo
  • anstream 0.6.14
  • anstyle 1.0.7
  • anstyle-parse 0.2.4
  • anstyle-query 1.1.0
  • anstyle-wincon 3.0.3
  • anyhow 1.0.86
  • autocfg 1.3.0
  • bitflags 2.6.0
  • byteorder 1.5.0
  • cfg-if 1.0.0
  • clap 4.5.8
  • clap_builder 4.5.8
  • clap_lex 0.7.1
  • colorchoice 1.0.1
  • condtype 1.3.0
  • console 0.15.8
  • crossbeam-deque 0.8.5
  • crossbeam-epoch 0.9.18
  • crossbeam-utils 0.8.20
  • divan 0.1.14
  • divan-macros 0.1.14
  • either 1.13.0
  • encode_unicode 0.3.6
  • errno 0.3.9
  • fxhash 0.2.1
  • getrandom 0.2.15
  • indicatif 0.17.8
  • instant 0.1.13
  • is_terminal_polyfill 1.70.0
  • itertools 0.11.0
  • itertools 0.13.0
  • lazy_static 1.5.0
  • libc 0.2.155
  • linux-raw-sys 0.4.14
  • num 0.4.3
  • num-bigint 0.4.6
  • num-complex 0.4.6
  • num-integer 0.1.46
  • num-iter 0.1.45
  • num-rational 0.4.2
  • num-traits 0.2.19
  • number_prefix 0.4.0
  • portable-atomic 1.6.0
  • ppv-lite86 0.2.17
  • proc-macro2 1.0.86
  • quote 1.0.36
  • rand 0.8.5
  • rand_chacha 0.3.1
  • rand_core 0.6.4
  • rayon 1.10.0
  • rayon-core 1.12.1
  • regex-lite 0.1.6
  • rustix 0.38.34
  • strsim 0.11.1
  • syn 2.0.68
  • terminal_size 0.3.0
  • unicode-ident 1.0.12
  • unicode-width 0.1.13
  • utf8parse 0.2.2
  • vers-vecs 1.3.3
  • wasi 0.11.0+wasi-snapshot-preview1
  • windows-sys 0.48.0
  • windows-sys 0.52.0
  • windows-targets 0.48.5
  • windows-targets 0.52.5
  • windows_aarch64_gnullvm 0.48.5
  • windows_aarch64_gnullvm 0.52.5
  • windows_aarch64_msvc 0.48.5
  • windows_aarch64_msvc 0.52.5
  • windows_i686_gnu 0.48.5
  • windows_i686_gnu 0.52.5
  • windows_i686_gnullvm 0.52.5
  • windows_i686_msvc 0.48.5
  • windows_i686_msvc 0.52.5
  • windows_x86_64_gnu 0.48.5
  • windows_x86_64_gnu 0.52.5
  • windows_x86_64_gnullvm 0.48.5
  • windows_x86_64_gnullvm 0.52.5
  • windows_x86_64_msvc 0.48.5
  • windows_x86_64_msvc 0.52.5
Cargo.toml cargo
  • divan 0.1.14 development
  • clap 4.5.7
  • fxhash 0.2.1
  • indicatif 0.17.8
  • itertools 0.13.0
  • num 0.4.3
  • phylo 0.1.0
  • rand 0.8.5