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phigis

PCR primer design

phisigns

PhiSiGns is a web-based and standalone application that provides a simple and convenient tool to identify signature genes and design primers for PCR amplification of related genes from environmental samples

phyds

Phylogenetic iDentification of Subgenomes

phylocsf

Phylogenetic analysis of multi-species genome sequence alignments to identify conserved protein-coding regions

phylogenies

Generate evolview and iTOL scripts to plot parameters from VCF file and metadata on the tree. These codes were made as a part of the Center for whole genome sequencing for MTB (CWGSMTB) project. https://www.cwgsmtb.com

phylogenomics_pipeline

After gene family clusing using Orthofinder, single copy nuclear genes and low copies nuclear genes were used to infer the phlogenies between related taxon, three types of data or algorithms were implemented to achive this goal. the perl script phylogenomics_4dtv.pl inferred the phylogeny using four-fold degenerated sites (4DTvs) of combined single copy nuclear genes;

phyltr

Phylogenetic Analysis of Long Terminal Repeat Retrotransposons

phyluce

software for UCE (and general) phylogenomics

phytophthora

Scripts used in the analysis of Phytophthora genomes

phytophthora_fragariae

Commands used in the analysis of P. fragariae genomes

picard

A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

pincer

In Silico PCR for Python3

pipa_parva

Sex determination in Pipa parva

pipeline-for-isoseq

A pipeline for isoseq

pipeline-for-isoseq-1

pipeline-for-lncrnas

a pipeline for identification and differentially expressed analysis of long non-coding RNAs

planttribes

PlantTribes is a collection of automated gene family analysis pipelines for comparative plant genomics

plit

plncpro

Prediction of plant lncRNAs using random forest

plot_data

这个是我画图的一些数据和代码还有结果

plot_mitochondrial_genome_with_circos

plws

Phylogenomics from Low-coverage Whole-genome Sequencing

pocketbook_database

polycracker-unofficial-mirror

A robust method for the unsupervised partitioning of polyploid subgenomes by signatures of repetitive DNA evolution https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-5828-5

polyprimer

Tool in Perl for finding Polymorphisms in primers for human genes.

polyrad

Genotype Calling with Uncertainty from Sequencing Data in Polyploids

polysat

polysat 1.7: tools for polyploid microsatellite analysis

pophelper

An R package to analyse and visualise admixture proportions from STRUCTURE, fastSTRUCTURE, TESS, ADMIXTURE etc.

poplddecay

PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format(VCF) files

popoolation2

Automatically exported from code.google.com/p/popoolation2