Posts
- Category: PCR / Primer Design (continued)
- HTP-OligoDesigner - An Online Primer Design Tool
- HTqPCR 1.13.0 - Analysis of High-throughput Quantitative Real-time PCR data
- HYDEN - A software for Designing Degenerate Primers
- In-Silico PCR 34 - Searches a Sequence Database with a pair of PCR Primers
- JCVI Primer Designer 20101122 - High Throughput PCR Primer Design
- jPCR 1.15.8 - Java Tools for PCR, in silico PCR, Oligonucleotide Assembly & Analysis
- KLab-PCR - Quantify the Starting Template in a PCR Reaction
- LAMP Designer 1.16 - Design Primers for Loop-Mediated Isothermal Amplification Assays
- LinRegPCR 20210614 - Analysis of Quantitative PCR Data
- MaxAlike 1.0 - Phylogenetic Reconstruction of incomplete Sequences by Maximum Likelihood
- MEDUSA - Selection and Visual Assessment of PCR Primer Pair
- MeltCalc 2.0 - Thermodynamic Probe Design
- MFEprimer 3.2.1 - PCR Primer Specificity Checking Program
- miniPCR 2.1 - Monitor and Analyze your PCR experiments
- MPprimer 1.5 - Reliable Multiplex PCR Primer Design
- mPrimer3 1.0 - Modification of Primer3
- MRPrimerW2 - Search valid Primers for multiple Targets of qPCR experiments without matching Off-targets
- MultiPLX 2.1 - Analyze PCR Primer Compatibility
- Mutagenesis Primer Generator - Generate Mutagenesis Primer
- NetPrimer - Free Primer Analysis Software
- NoePrimer 3.0 - Primer Design Software
- nondetects 2.22.0 - Model and Impute non-detects in qPCR data
- NormFinder 0.953 - Normalization of Real-Time Quantitative Reverse Transcription-PCR Data
- Oligo 7.60 - Primer Analysis Software
- Oligo Heat Map 1.52 - Check Thermodynamical Parameters for PCR primers
- OligoCalc 3.26 - Oligonucleotide Properties Calculator
- OligoFaktory SE - Oligonucleotide Design
- OligoLocator 1.0 - Oligonucleotides Analysis
- Oligospawn - Oligo Design from large-scale cDNA Sequences
- Optimus Primer - Primer Design for large-scale Resequencing by Second Generation Sequencing
- ORFprimer 1.6.4.1 - High Throughput PCR Primer Design
- PCR Analyzer v 1.02 - Estimate for Initial Amount of Amplicon Present in a PCR
- pcrcoal 1.2.0 - Coalescent Simulations of PCR
- PCRduplicates - Estimate PCR Duplication Rate from High-throughput Sequencing data
- PCRsetup - Tool for Planning PCR and qPCR Reactions
- PD5 1.5 - Software Library for the Development of Primer Design Applications
- PerlPrimer 1.1.21 - Open-source PCR Primer Design
- PhiSiGns 1.2 - Indentify Signature Genes in Phages and Design Primers
- PolyMarker - Fast Polyploid Primer Design Pipeline
- PrimeDesign 0.2 - Flexible Design of pegRNAs and ngRNAs for Prime Editing
- Primegens 2.0.5 - Primer Design for Microarray
- Primer Premier 6.25 - PCR Primer Design Software
- Primer Prim'er 5.6.0 - PCR Primer Design Tool
- Primer3 2.4.0 / Primer3-web 4.1.0 / Primer3Plus 2.5.0 - PCR Primer Design Tool
- primerD 1.0 - Design of Unique Degenerate Primer Pairs
- PrimerDesign-M - Multiple-alignment based Multiple-primer Design tool
- PrimerDesigner 1.7 - Design PCR Primers
- PrimerFactoryQt 1.0.3 beta- Tool for Searching and Designing Primers
- PrimerHunter 1.0.2 - Primer Design for PCR-Based Virus Subtype Identification
- Primerize 1.0 - PCR Assembly Primer Design
- PrimerPlex 2.76 - Oligo Design for Multiplex PCR
- PrimerProspector 1.0.1 - Design and Analyze PCR Primers
- PrimerPy 0.97a - GUI tool for QPCR Primer Design
- PrimerSelect - Computes the AES score for each position in a Genome given a random Primer 5' tag
- PrimerSeq 1.1.12 - Primer Seek in RNA-Seq
- PrimerStation - Multiplex PCR Primer Design site
- PrimerZ 20171130 - Streamlined Primer design for Promoters, Exons and Human SNPs
- PRISE - Designing Sequence-selective PCR Primers
- PriSM - Primer Selection and Matching for Amplification of Viral Genomes
- ProbeMaker 1.4.1 - Design and Analysis of sets of Oligonucleotide Probes
- PROBER 2.1 - Fish Oligo Probe Design Software
- ProbeSpec - Map Specificity of all Candidate Probes for a Given Sequence
- prsrch 0.51 - Simple tool for Primer Design
- Pythia 1.0.1 - Thermodynamically based PCR primer design program
- Q-Gene 1.2 - Process Quantitative Real-time RT-PCR Data
- qbasePLUS 2.0 - Real-time PCR Data Analysis
- qcalculator 1.0 - Calculate Relative mRNA Gene Expression
- QDD 3.1.2 / QDD-VM 3.1.2 - Select Microsatellite Markers and Design Primers
- QPCR 1.0 - Store, Manage, and Analyze data from qPCR Experiments
- qPCR-DAMS 1.2 - Analyze, Manage, and Store Quantitative Real-Time PCR data.
- qRTDesigner 1.2 - Designing Primers for Real-time Quantitative PCR Assays
- QUALITY 1.1.6 - Variant of the minimum Chi-squared method for limiting Dilution Assays
- QUMA 1.1.13 - Visualize and Quantify Bisulfite Sequence data for CpG Methylation Analysis
- ReadqPCR / NormqPCR 1.38.0 / - Read qPCR data / Functions for Normalisation of RT-qPCR data
- Realyser 1.0 - Real Time PCR Normalisation tool
- RJPrimers 1.0 - Transposable Element Junction based PCR Primer Design
- SARS - Statistical Analysis of Real-time PCR Software
- SeqState 1.4.1 - Primer Design, Sequence Statistics & Indel Coding
- SLICSel 1.1 - Design Specific Oligonucleotide Probes for Microbial Detection and Identification
- StarPrimer D’Signer 3.0.0.3 - Design of Primers for ENTRY Cloning to Create Donor Vector
- unifiedWMWqPCR 1.28.0 - Unified Wilcoxon-Mann Whitney Test for testing differential Expression in qPCR data
- UniPrime2 2.10 - Universal Primer Design Server
- Category: Phylogenetic Analysis
- abioscripts - Facilitating Phylogenetic Analysis
- AdaptML 1.0 - Partitioning of Gene Sequences according to their Genetic and Ecological Similarity
- ADAPTSITE 1.6 - Detect Natural Selection at Single Amino Acid Sites
- adephylo 1.1-11 - Exploratory Analyses for the Phylogenetic Comparative Method
- ADseq - Comparative Scaffolding
- Agalma 1.0.0 - A Transcriptome Assembly and Phylogenetic Analysis Environment
- AHLC - Adhockeries for Estimating Divergence Times between Species
- Alfacinha - Simulation of Sequence Evolution with Neighbouring-site Dependencies
- ALFRED-G - Distance Estimator for Phylogenetic Inference
- AlgorithmTreeFromLabels 1.0 - Creat Nexus files from Classificatory Language labels
- ALIFRITZ 1.0 - Statistical Multiple Alignment and Phylogeny Reconstruction
- ALTREE 1.3.1 - Phylogeny-based Analysis
- AMPHORA2 - Automated Phylogenomic Inference Pipeline for Bacterial and Archaeal Sequences
- AmphoraNet - Metagenomic and Genomic Analysis tool (AMPHORA2)
- AmphoraVizu - Chart Visualization for Metagenomic and Genomic Analysis tools AMPHORA2 and AmphoraNet
- Anc-gene - Inference of Ancestral Gene Sequences by the Distance-Based Bayesian Method
- ANCESCON - ANCEStral sequence reCONstruction
- Ancestor - Inference of Ancestral Amino Acid Sequences by the Distance-Based Bayesian Method
- ANCML 1.0 - Ancestor States using Maximum Likelihood
- ANGST - ANalyzer of Gene and Species Trees
- AntigenicTreeTools 1.0 - Infer Antigenic Trees to resolve the Antigenic Impact of Amino Acid Changes
- APE 5.5 - Analysis of Phylogenetics and Evolution
- apTreeshape 1.5-0.1 - Analyses of Phylogenetic Treeshape
- ArboDraw 2006 - Phylogenetic Tree Builder & Viewer
- Archaeopteryx 0.9928 - Visualization, Analysis & Editing of Phylogenetic Trees
- Armadillo 1.1 - A simple pipeline system for Phylogenetic Analysis
- ASILA - Constructive Perfect Phylogeny Matrix Algorithm
- ASTRAL 5.7.1 - Accurate Species TRee ALgorithm
- AtvEditor 1.1.0 - A Tree Viewer
- AutoMatrix - Calculate an Instantaneous Rate Matrix
- AxParafit / AxPcoords - Highly optimized and Parallelized version of Parafit / DistPCoA
- BaCoCa 1.1 - Heuristic software tool for Parallel Assessment of Sequence Biases in hundreds of Gene and Taxon Partitions
- BADGER 1.02 beta - Bayesian Analysis of Phylogenies
- BAli-Phy 3.6.0 - Bayesian Alignment and Phylogeny estimation
- BAMBE 4.01a - Bayesian Analysis of Phylogenies
- Baobab 3.31 - Editor for Large Phylogenetic Trees
- barphlye – Bayesian Rearrangement Phylogeny in Yersinia
- BaTS 1.0 - Measure and Test Phylogeny Trait Associations
- Bayes - Modeling Incomplete Alignments in Phylogenetic Inference
- BayesPhylogenies 1.1 - Inferring Phylogenetic Trees using MCMC or MCMCMC
- BayesTraits 2.0 beta - Analyses of Trait Evolution among groups of Species
- BayesTrees 1.3 - Display Samples of Trees, in particular Bayesian samples
- bdvis 0.2.28 - Biodiversity Data Visualizations
- BEAGLE 3.1.2 - Evaluating the Likelihood of Sequence Evolution on Trees
- BEAST 1.10.4 / BEAST2 2.6.1 - Bayesian Evolutionary Analysis of Molecular Sequences
- BEGFE 1.1 - Bayesian Estimation of Gene Family Evolution
- BEST 3.0 - Phylogenetic Analysis of Multilocus Data
- BIONJ - Distance based Phylogeny Reconstruction Algorithm
- BitPhylogeny 0.99 - Reconstruct Intra-tumor Evolutionary Pathways
- BMGE 1.12 - Selection of Phylogenetic Informative Regions from Multiple Sequence Alignments
- BN-BS - Estimation of Synonymous and Nonsynonymous Branch Lengths from Pairwise Distances
- BootFam - Define Gene/Protein Families
- Bosque 2.0.2 - Phylogenetic Analysis Software
- BPandP 4.4.0 - Bayesian MCMC algorithms for the analysis of Phylogeographic DNA data
- BPhyOG 1.0 - Bacterial Phylogenies based on Overlapping Genes
- BranchClust 1.01 - A Phylogenetic Algorithm for Selecting Gene Families
- BUCKy 1.4.4 - Gene Tree Reconciliation with Bayesian Concordance Analysis
- Burntrees 0.3.3 - Perl script for manipulating MrBayes tree and Parameter files
- BYPASSR 1.0 / BYPASSR-DEGR 1.0.2 - Bayesian Phylogenetic Analysis of Site-Specific Rate / with a model for Post Mortem Modification
- CAIC v.2.6.9 / MacroCAIC - Calculates Phylogenetically Independent Contrasts in one or more Variables
- CAPE - Test Convergent and Parallel Evolution at the Amino Acid sequence level
- CAT/BAT v5.2.3 - Taxonomic Classification of Contigs and Metagenome-assembled Genomes
- CBCAnalyzer 1.1 beta - Inferring Phylogenies based on Compensatory Base Changes
- CCD 1.0 - Core Collection of Diverse Taxa
- CDTree 3.1 - Protein Domain Hierarchy Viewer and Editor
- Ceiba 1.05 - Scalable Phylogeny Visualization with Images
- CellScape 0.99.3 - Visualization tool for integrating single Cell Phylogeny
- CensuScope 1.2 - Detect Taxonomic Composition of a Metagenomic Data Set
- CGHdist 1.0 - Calculates Mximum Likelihood-based Distances from Gene Content
- chromEvol 2.0 - Analyze Changes in Chromosome-number along a Phylogeny
- CITUP v0.1.0 - Clonality Inference in Multiple Tumor Samples using Phylogeny
- CladeAge - Divergence Prior Distributions based on a probabilistic model of Fossil Preservation
- clan_check v1.3 - Check Trees for compatibility with Defined Clans
- Clann 4.2.5 - Construct Phylogenetic Supertrees
- CLIME v1.1 Beta - Clustering by Inferred Models of Evolution OMIM results
- ClockstaR 2.0.1 - Choosing the number of Relaxed-clock models in Molecular Phylogenetic Analysis
- COAL 2012 - computing Gene Tree Probabilities under the Coalescent process
- Coala 1.2.1 - COevolution Assessment by a Likelihood-free Approach
- coalator 1.1- Interactive Drawing of Coalescent Trees
- COALGF Calculator 1.0 - Computing Probabilities of Gene Tree Histories Given Species Trees Under the Coalescent Process with Gene Flow
- Cocos - Reconstructing Phylogenies of Multi-Domain Proteins
- codonbias 20060818 - Estimate Selection Coefficients relating to optimal Codon usage
- CodonPhyML 1.00 - Phylogeny Inference under Codon Models using Maximum Likelihood
- CoEv 1.1.7 - Predicts Coevolving Positions and their Evolutionary Profile
- CoevRJ - Jointly Estimate Phylogeny and Molecular Coevolution
- CoMap 1.5.2 - Map Substitutions on a Phylogeny and Detect Coevolution
- CombineTrees - Unite MP Trees into Single Graph
- ComPhy - Genome Composite Distance Phylogeny for whole-genome phylogeney inferences
- COMPONENT 2.0 - Analysis of Evolutionary Trees
- CompPhy - A Web-based Collaborative Platform for comparing Phylogenies
- Consel 0.20 - Assess Confidence of Phylogenetic Tree Selection
- Conserve IV 1.4b - Assess & Prioritorize Conservation Schemes based on Phylogenies
- CoPAP 201204 - Co-evolution of Presence-Absence Patterns
- CopyCat 2.04 - Co-phylogenetic Analysis Tool
- CoSpec - Show Coevolutionary Behaviours of Two Phylogenies
- Count 10.04 - Evolutionary Analysis of Phylogenetic Profiles and Other Numerical Characters
- covarionTest 20050610 - Covarion Structure Test
- CowPI - A rumen microbiome focussed version of the PICRUSt Functional Inference software
- CR_Pipeline - Solve the Character Removal (CR) Problem for the Multistate Perfect Phylogeny Problem
- creto 1.0 - Determination of Cis-Regulatory Element Turn-Over rates
- CRIMSON 2.1.3 beta - Subtree Extraction from very large Phylogenetic Trees
- CSSSCL 1.0 - A Taxonomic Classifier for DNA Sequences.
- CTree 1.03 - Analysis of Clusters on Phylogenetic Trees
- CVTree 4.0 - Construct Prokaryotic Phylogency Tree by using Composition Vector Approach
- DARwin 6.0.021 - Diversity and Phylogenetic Analysis
- DASACT - Decision Aiding Software for Axiomatic Consensus Theory
- DeClone - Evolutionary Scenarios for Gene Adjacencies in a Gibbs-Boltzmann framework
- DeCo - Evolution of Gene Neighborhoods
- DeCoLT - Lateral Gene Transfer, Rearrangement, Reconciliation
- DeCoStar - Reconstructing Parsimonious histories of Gene Adjacencies
- DendroPy v4.5.1 - Phylogenetic Computing Library
- Dendroscope 3.7.6 - Visualize Phylogenetic Trees & Rooted Networks
- DensiTree 2.2.3 - Qualitative Analysis of Sets of Trees
- DISPAN - Genetic Distance and Phylogenetic Analysis
- Distance 1.0 - Estimation of Reversible Substitution Matrices and Evolutionary Distance
- Distory 1.4.4 - Distance Between Phylogenetic Histories
- DIVEIN - Analyze Phylogenies, Sequence Divergence, Diversity and Informative Sites
- DiverAnalysis - Analysis of Sequence Divergence and Diversity
- diversitree 0.9-15 - Comparative Phylogenetic Analysis of Diversification in R
- DLCoal 1.0 - Modeling Gene Duplications, Losses, and Coalescence
- DLCpar v1.1 - Reconciles Gene Trees to Species Trees through Maximum Parsimony
- drawStrees 1.2 - Interactive Drawing of Generalized Suffix Tree
- DrML 1.0 - Maximum Likelihood Estimation in the Duplication Loss Model
- DTL-RnB - Summarizing the Space of DTL Reconciliations
- DTscore - Fast and Accurate Distance Algorithm to Reconstruct Tandem Duplication Trees
- DupliPHY 2.0 / DupliPHY-ML 1.2 - Determine the Evolutionary Histories of Gene Families
- DupLoCut - Duplication Loss Phylogeny by Cutting Planes
- DupTree - Large Scale Gene Tree Parsimony Analysis
- DynaDup 2.3.2 - Inferring Optimal Species Trees under Gene Duplication and Loss
- EBD 1.0.8 - Taxon- and Phylogenetic-based Beta Diversity Measures
- ecceTERA 1.2.4 - Gene Tree Species Tree Reconciliation
- EDIBLE 20110705 - Make Phylogenetic Information Calculations
- EEEP 1.01 - Efficient Evaluation of Edit Paths
- EMRAE - Efficient Method to Recover Ancestral Events
- EPoS 0.91 - Estimating Phylogenies of Species
- ERATE 0.8 - Maximum Likelihood Phylogenetic Inference
- eShadow - Phylogenetic Shadowing
- ETE 3.1.1 - Python Environment for Phylogenetic Tree Exploration
- Eucalypt 1.0.4 - EnUmerator of Co-evolutionary Associations in PoLYnomial-Time delay
- EvolView v3 - An Online Phylogenetic Tree Viewer and Customization Tool
- ExaBayes 1.5 - Parallelized Bayesian Tree Inference for large-scale datasets
- ExaML 3.0.21 - Large-scale Phylogenetic Inference on Supercomputers using MPI
- FamFetch 2.0 - Search for Tree Patterns in Databases of Phylogenetic Trees
- FastCodeML 1.1.0 - Fast Detection of Positive Selection on Phylogenetic Trees
- fastHN - Fast Tool for Minimum Hybridization Networks
- FastME 2.1.5 - Fast & Accurate Phylogeny Reconstruction
- FastML 201401 - Server for computing Maximum Likelihood Ancestral Sequence Reconstruction
- fastphylo 1.0.3 - Fast tools for Phylogenetics
- FastTree 2.1.11 - Cmpute Large Minimum Evolution Trees with Profiles
- Fasturec 201605 - Local Search algorithms for Gene Tree Parsimony problems
- FFP 3.19 - Feature Frequency Profile Phylogeny
- FigTree 1.4.4 - Produce Figures of Phylogenetic Trees
- Filo 1.1 - Simulate Sequence Data used in Phylogenetic Analyses
- FISHER - Fisher's Exact Test for 2x2 Tables
- FISHtrees 3.2.0 - Phylogenetic Analysis of Multiprobe Fluorescence in situ Hybridization data
- FitchAln 20100321 - Given Phylogenetic Tree and Multiple Sequence Alignment, show the Fitch Score Matrix
- Fitmodel 20131125 - Deciphering the Patterns of Darwinian Selection
- FlowerPower - Clustering algorithm for Identification of Global Homologs
- forester 1.038 - Software Libraries for Phylogenomics and Evolutionary Biology Research
- FPSAC 1.0 - Comparative Scaffolding of Ancient Contigs.
- FSTAT 2.9.3.2 - Estimate & Test Gene Diversities
- FTreeView 1.1.0 - Functional Treeview
- G-PhoCS - Generalized Phylogenetic Coalescent Sampler
- GARLI 2.0.1 - Phylogenetic Analysis of Molecular Sequence data using the Maximum-likelihood Criterion
- Gblocks 0.91b - Selection of Conserved Blocks from multiple alignments for their use in Phylogenetic Snalysis
- GEIGER 2.0.7 - Analysis of Evolutionary Diversification
- GeLL 2.0 - General Likelihood Library for use in Phylogenetics
- GeneRax 1.0.0 - Maximum Likelihood based Gene Tree Inference
- GeneTree 1.3 - Compare Gene and Species Trees
- Genetree 9.0 - Software for Ancestral Inference.
- GenGIS 2.5.3 - Combine Digital Map data with Genomic Data
- Genie 3.0 - Estimating Demographic History from Molecular Phylogenies
- GenomeSignatureTree 1.0 - Alignment-free Inference of Genome Trees
- GEODIS 2.6 - Nested Clade Phylogeographic Analysis
- GeoMeTree 1.1 - Geodesic Metric on Trees
- GeoPhyloBuilder 1.2.1 - ArcGIS Extension that Creates Geophylogenies
- GFICLEE 1.0 - Gene Function Inferred by Common Loss Evolutionary Events
- GGDC 3.0 - Genome-to-Genome Distance Calculator
- ggtree 2.0.0 - Phylogenetic Tree Viewer for Different Types of Tree Annotations
- GIGA 1.4.1 - Gene Tree Inference in the Genomic Age
- Ginkgo 4.0.0 - Phylogeographical Evolution Simulator
- Gist 0.7.17 - Generative Inference of Sequence Taxonomy
- GLOOME 201305 - Gain Loss Mapping Engine
- GO4genome - Whole Genome Phylogeny
- GOTaxExplorer 1.0 - Tool for Querying GOTaxDB
- GPU MrBayes 3.2.6 - MrBayes on a Graphics Processing Unit
- GPX - Gene Phylogeny eXplorer
- GraphDTL v004 - Graph Reconciliation for Species Tree S and Gene Tree G
- GRAPPA 2.0 - Genome Rearrangements Analysis under Parsimony and other Phylogenetic Algorithms
- GRate 1.0 - Relative Rate Test for Groups of Taxa Using General DNA Substitution Models in PAUP*
- GRUNT - Grouping Ungrouping Naming Tool
- GZ-gamma - Estimate Parameter of Substitution Rate Variation among Sites
- HapReads - Infering Haplotypes with Shot Reads
- HGT_simul 1.2 - Phylogenomic Simulation
- Hieranoid 2.0 - Hierarchical Orthology Inference
- HTTMM - Hierarchical Taxonomy Tree based Mixture Model
- HybridNet - Compute rSPR Distances, Hybridization Numbers, and Hybridization Networks
- HyperGeny - View Large Phylogenetic Trees
- HyperTree 1.2.2 - Java Phylogenetic Tree Viewer
- HyPhy 2.5.31 - Hypothesis testing using Phylogenies
- iBPP v2.1.3 - Bayesian Species Delimitation Integrating Genes and Traits data
- iGTP 1.1 - Infer Species Phylogenies from Gene Phylogenies
- ImOSM 20110902 - Imbed model Violation as One Step Mutations into Sequence Alignment
- IPP / IPPH - Algorithms for Incomplete Perfect Phylogeny Haplotyping
- IQ-TREE 1.6.12 / W-IQ-TREE - Efficient Phylogenetic Tree Reconstruction and ultrafast Bootstrap Approximation
- IQPNNI 3.3.2 - Reconstruct a Phylogenetic Tree based on DNA or Amino Acid Sequence data
- iTOL 5.2 - Display & Manipulation of Phylogenetic Trees
- iTree - Immunopeptidome-based Tree of Life
- iTree 2 - Scalable Multithreaded Phylogenomic Pipeline
- ivy - Interactive Visual Phylogenetics
- Jane 4.01 - Cophylogeny Reconstruction
- JET - Predict Protein Interfaces based on Sequence Sampling
- Jevtrace 3.16b - Implementation of Evolutionary Trace
- jMODELTEST 2.1.10 - Phylogenetic Model Averaging
- JolyTree 2.1 - Fast Distance-based Phylogenetic Inference from unaligned Genome Sequences
- JPrIME 0.3.7 - Bayesian Phylogenetics Library in Java
- jsPhyloSVG 1.55 - Javascript Library for Visualizing Interactive & Vector-based Phylogenetic Trees
- JTreeView 0.8 - Java based Phylogenetic Tree Viewer
- kdetrees 0.1.5 - Nonparametric method for identifying Discordant Phylogenetic Trees
- Kinome-render 1.3 - Visualize the Protein Kinase Superfamily of Protein
- Kraken 1.1.1 - Kraken Taxonomic Sequence Classification System
- Ktreedist 1.0 - Calculation of the Minimum Branch Length Distance (K tree score) between Phylogenetic Trees
- Lagrange 20130526 - Likelihood Analysis of Geographic Range Evolution
- LAMARC 2.1.10 - Maximum Likelihood & Bayesian Estimation of Population Parameters
- LAPD - Estimate Protein Distances
- LcaMap - Simultaneous Identification of Duplications, Losses and Lateral Gene Transfers
- Leaphy 1.0 beta - Phylogenetic Tree Estimation Software
- LGTNet 1.0 - Fast inference of lateral Genetic Transfer Networks
- LICHeE 1.0 - Multi-sample Cancer Phylogeny Reconstruction
- LINTREE - Test Molecular Clock and Make Linearized Trees
- LSD - Levels of exclusively Shared Differences
- LumberJack 7.10 - Analyzing the Phylogenetic Signal in Regions of Multiple Sequence Alignments
- lyne 0.1.3 — Lineage Dynamics for Epigenetics
- Mac5 1.7.3 - Phylogenetic Reconstruction using Gapped Data
- MacClade 4.08a - Phylogenetic Analysis
- Mailfit 0.2 - Perl script that runs PAUP and MrModeltest2
- map_dp - Factorize Branchlengts
- MAPPS 1.1.6 - Determine Nucleotide Model Adequacy
- markophylo 1.0.7 - Markov Chain Models for Phylogenetic Trees
- MASTtreedist 1.0 - Visualization of Tree Space based on Maximum Agreement Subtree
- Mavric 0.8.3 - Python toolkit for Phylogenetics
- MaxSubTree - Detect Coevolved Amino Acid Networks in Protein Families of Variable Divergence
- MaxTiC - Ranking Nodes in a Phylogeny using inferred Horizontal Gene Transfers
- MC-NET 1.0 - Construction of Phylogenetic Networks
- MCQ-Net - Constructing Phylogenetic Networks from Weighted Quartets
- MDL 1.0 - Minimum Description Length for the detection of Phylogenetics Breakpoints
- MEDICC - Minimum Event Distance for Intra-tumour Copy number Comparisons
- MEGA 11 - Molecular Evolutionary Genetics Analysis
- mesquite 3.6.1 - Modular System for Evolutionary Analysis
- metaBIT 1.1 - automated Microbial Taxonomic Profiling
- MetaPASSAGE - Automated Simulations and Analysis of Gene Families
- MetaPIGA v3.1 - Large Phylogeny Estimation
- MetaTreeMap 3.2 - An Alternative Visualization Method for Displaying Metagenomic Phylogenic Trees
- METREE 1.2 - Infer and Test Minimum Evolution Trees
- MfstMiner - Enumerating All Maximal Frequent Subtrees
- MirrorT 0.1 - Mirroring Co-evolving Trees in Light of their Topologies
- Mirrortree - Interactive study of the Co-evolution of Protein Families
- misfits 1.0 - Evaluate Goodness of Fit between Phylogenetic Model and Alignment
- MitoPhAST 3.0 - Mitogenome Phylogenetic Analysis of Sequences Tool
- MixMapper 2.0 - Admixture Parameter and Topology Inference using Allele Frequency Divergences
- MJOIN 1.2 - Neighbor Joining with Subtree Weights
- MLGO - Maximum Likelihood for Gene Order Analysis
- MLS 1.0 - Amalgamating Source Trees with Different Taxonomic Levels
- MLTreeMap 2.061 - Phylogenetics and Functionalities of Metagenomes
- ModelGenerator 0.851 - Amino Acid & Nucleotide Substitution Model Selection
- ModelPie 1.01 - GUI for ModelTest and MrModelTest
- ModelTest-NG 0.1.6 - The all new faster ModelTest, superseding jModelTest and ProtTest
- Monophyler 1.0 - Monophyly of a sample of Gene Lineages on Species Tree
- morePhyML 1.14 - Improving ML tree searching with PhyML 3
- motifStack 1.34.0 - Visualization of Motif Alignment and the analysis of Transcription Factor Binding site Evolution
- Mowgli v2 - Phylogenetic Tree Reconciliation Program
- MP-EST 2.0 - Estimating Species Trees from a set of Gene Trees
- MPI-PHYLIP - Parallelizing Computationally Intensive Phylogenetic Analysis
- MrAIC 1.4.6 / pMrAIC 1.1 - Perl script for selecting DNA substitution models using PHYML
- MrBayes 3.2.7a - Bayesian Inference of Phylogeny
- mrc.py 1.0 - Compatibility Lengths of Supertrees and Gene Trees
- MrModelfit 1.2/ Modelfit 1.2 - Perl script for running MrModeltest2/Modeltest
- MrModeltest 2.3 - C program for selecting DNA substitution models using PAUP*
- mswordtree 1.0 - MS Word Macro for Drawing of Phylogenetic Trees
- mtree - Reticulate Networks of Multiple Phylogenetic Trees
- MTRT - Multilabled Tree from Rooted Triplets
- MulRF 1.2 - Phylogenetic Analysis using Multi-copy Gene Trees
- MultiTypeTree 7.0.1 - Structured Population Inference for BEAST 2
- multperf - Generate the Empirical Results on the missing data problem in multi-state perfect Phylogenies
- MY-CLOSURE 1.0 - Computing a Phylogenetic Network from a collection of Phylogenetic Trees
- MySSP 1.0.3.5 - Simulation of DNA Sequence Evolution across a Phylogenetic Tree
- MyTaxa - Assign Taxonomy to Metagenomic Fragments
- NCL 2.1.18 - NEXUS C++ Class Library
- NDE 0.5.0 - NEXUS Data Editor
- Network 10.2.0.0 - Phylogenetic Network Software
- NetworkDiversity 1.0.0 - Calculation of beta diversity over Phylogenetic Networks
- NewickReader 1.0 - Produce Distance Matrix from Branch Lengths in Phylogenetic Tree
- newicktree 1.1 - LaTeX package for Drawing of Phylogenetic Trees
- NG-new - Modified Nei-Gojobori Method for Computing Synonymous and Nonsynonymous Distances
- nhPhyML - Compute Phylogenetic Trees under non Homogeneous model of DNA sequence Evolution
- NimbleTree 2.6 - Make Phylogenetic Trees from Sequence Data
- NJplot 2.4 - Phylogenetic Tree Drawing Program
- Notung 2.6 - Date Gene Duplications and Optimizing Gene Family Trees
- opph 1.0 - Perfect Phylogeny Haplotyping
- ORFanFinder - Identification of Taxonomically Restricted Orphan Genes
- Ortholuge 0.8 - Improve Specificity of High-throughput Ortholog Prediction
- OrthoSelect - Selection of Orthologs in Phylogenomics
- P4P - Peptidomes for Phylogenies
- Padre 2.0 - Package for Analyzing and Displaying Reticulate Evolution
- PAINT 2.24 - Phylogenetic Annotation and INference Tool
- PAL 1.5.1 - Java Library for Molecular Evolution & Phylogenetics
- PAML 4.8a / PAMLX 1.3.1 - Phylogenetic Analysis by Maximum Likelihood
- PaPaRa 2.5 - PArsimony-based Phylogeny-Aware Read alignment program
- ParalogyCorrector - Gene Tree Correction
- ParGenes 1.1.0 - Model Selection and Tree Inference on thousands of Genes
- Parsimonator 1.02 - Fast open-source Parsimony program
- PASSML / Passml_TM - Analysis of Phylogeny / Transmembrane Domain searching from Aligned Amino Acid Sequences
- PASTA 1.8.6 - Practical Alignment using SATé and TrAnsitivity
- PASTRI 0.1 - Probabilistic Algorithm for Somatic TRee Inference
- PATHd8 - Phylogenetic Dating of Large Trees without Molecular Clock
- PATHGROUPS - Rapid Small Phylogeny
- Patristic - Input different Tree files and computes their Patristic Distances
- Paup GUI 2011 - User-friendly Interface to Phylogenetic program PAUP*
- PaupUp 1.0.3.1 - Graphical Frontend for Paup* DOS software
- PDA 1.0.3 - Phylogenetic Diversity Analyzer
- Pebble 1.0 - Phylogenetic Analysis Application
- PEMS 6.6.4 - Phylogenetic Estimation of Metagenomic sequence using BLSOM
- pez 1.2-3 - Phylogenetics for the Environmental Sciences
- Phandango 1.1.0 - Interactive Visualization of Genome Phylogenies
- phangorn 2.7.1 - Phylogenetic Analysis in R
- PHASE 2.0 - Bayesian & Maximum Likelihood Phylogenetic Inference Package
- PHAST 1.5 / RPHAST 1.6.9 - Phylogenetic Analysis with Space/Time Models / for R
- PhEVER 2.0 - Viral Evolution and Virus/host Co-evolution
- PhISCS 1.0 - Tumor Phylogeny Reconstruction via Integrative use of Single Cell and Bulk Sequencing Data
- pHMM-Tree - Phylogeny of Profile hidden Markov models
- Phy2HTML 1.0.1 - Display Phylogeny using only HTML and CSS
- Phybase 2.0 - R package for Phylogenetic Analysis
- PhyBayes 200208 - Bayesian Inference in Phylogenetics
- Phycas 2.2.0 - Phylogenetic Analyses
- phyclust 0.1-30 - Phylogenetic Clustering
- PhyD* - Fast NJ-like algorithms to deal with incomplete Distance Matrices
- PhyDE2 0.2.0 - Phylogenetic Data Editor
- PhyDesign - Phylogenetic Informativeness Analysis
- phyl_util - Phylogenetic Utility Programs
- Phyla_AMPHORA - Phylum-specific Automated Phylogenomic Inference Pipeline for Bacterial Sequences
- PHYLDOG 2.0beta - Organism and Gene PHYlogenies Modeling Gene Duplications and Losses
- Phylemon 2.0 - Web-tools for Molecular Evolution, Phylogenetics, Phylogenomics and Hypothesis testing
- Phylip 3.695 - Free Package of Programs for Inferring Phylogenies
- Phylo-HMGP - Infer Heterogeneous Evolutionary States of Functional Genomic Features
- Phylo-HMRF - Comparing 3D Genome Organization in Multiple Species
- Phylo-MCOA 1.4 - Analysis of large Samples of Phylogenetic Trees
- Phylo-SMC r0 - Bayesian Phylogenetic Inference tool based on Sequential Monte Carlo
- PhyloAcc v1.0 - Bayesian Detection of Changes of Conservation of a Genomic Region
- PhyloAssigner 6.166 - Phylogenetic Classification of Amplicon Pyrosequences
- PhyloBayes 4.1c - Bayesian Phylogenetic software based on Mixture Models
- Phylobox beta - Phylogeny Viewer built for native use in HTML5 Web browesers
- phyloBreak - Gene Genealogy Simulator for Phylogeographic Study
- Phylocom 4.2 - Analysis of Phylogenetic Community Structure and Character Evolution, with Phylomatic
- PhyloCore - Phylogenetic approach to Identifying Core Taxa in Microbial Communities
- Phylodendron 0.8d - Phylogenetic Tree Drawing
- PhyloDet 1.0 - PhyloDetective tree visualizer
- phyloExpCM 0.32 - Phylogenetic Analysis with experimentally determined Codon Models
- Phylogen 1.1 - Simulate Phylogenies
- PhyloGena 1.04 - Automated Interactive Phylogenetic Annotation Tool
- phyloGenerator 1.3a - automated Phylogeny Generation for Ecologists
- PhyloGenie - Automating Phylome Analysis
- PhyloGeoRef - Java Library for Mapping Phylogenetic Trees and Geographical Information in KML
- Phylojive - Integrating Biodiversity data with the Tree of Life
- phylolm 2.6.2 - R package for Fitting Phylogenetic Linear Regression models
- PhyloMap 2.2.1 - Visualizing Relationships of large Sequence data sets to the influenza A virus genome
- PhyloMapper 1.0 beta 1 - Estimate Phylogeographic History using Genetic Data
- Phylomarker 3.0 - Mining Phylogenetic Markers for Assembling the Tree of Life
- phyloMeta 1.3 - Phylogenetic Comparative Analyses with Meta-analysis
- PhyloNetworks v0.14.2 - Analysis for Phylogenetic Networks
- Phylonium 1.4 - Fast and Accurate Estimation of Evolutionary Distances
- PhyloPars - Estimation of Missing Parameter Values using Phylogeny
- PhyloPat 52 - Phylogenetic Pattern analysis of Eukaryotic Genes
- PhyloPFP - Gene Ontology Prediction Using Phylogenomics
- PhyloPro - Generation and Visualization of Phylogenetic Profiles across Eukarya
- PhyloPythiaS 1.3 / PhyloPythiaS+ 1.4 - Web Server for Taxonomic Assignment of Metagenome Sequences
- PhyloQuart 1.4 - Reconstruct Phylogenies from Quartets
- phyloseq 1.27.6 / Shiny-phyloseq - Analysis of High-throughput Phylogenetic Sequence data
- PhyloSift 1.0.1 - Phylogenetic and Taxonomic Analysis for Genomes and Metagenomes
- PhyloSim 3.0.5 - Monte Carlo Simulation of Sequence Evolution
- PhyloSketch 0.1.8 - Sketch rooted Phylogenetic Trees and networks
- PhyloSNP - Take SNP data files (.csv and .vcf) and Generate Phylogenetic Trees
- PhyloSort 1.3 - Phylogenetic Sorting Tool
- phylostan - Phylogenetic Inference using Stan
- PHYLOSTAT 1.0b - Calculate Several Statistics from Phylogenetic Tree
- PhyloToL 3.0 - Phylogenomic Tree of Life
- phylotools 0.2.2 - Phylogenetic Tools for Ecologists
- PhyloTrack 2.1 - D3.js and JBrowse for Phylogeny and Positioning of Samples
- phylotree 1.0.0 - Collection of programs for Cophylogeny Testing
- PhyloTreePruner - A Nifty Java program for Pruning Phylogenetic Trees
- PhylOTU - Phylogenetic Clustering of Metagenomic Sequences into OTUs
- PhyloUtil 201302 - open-source Phylogenetic Tree Utilities
- PHYLOViZ 1.0 - Phylogenetic Inference and Data Visualization for Sequence based Typing Methods
- PhyloWidget - View, Edit, and Publish Phylogenetic Trees
- PHYLTEST 2.0 - Test Phylogenetic Hypothesis
- PhyML 2020 - Phylogeny software based on the Maximum Likelihood
- PhyML_Multi - Compute Phylogenetic Trees in cases where events of Homologous Recombination have Affected an Alignment
- PHYMMBL 4.0 - Taxonomically Classifying Metagenomic Short Reads
- PhyNav 1.0 - Reconstruct Evolutionary Relationship among Contemporary Species based on Genetic data
- PhyRe - Evaluate Taxon Sampling in Evolutionary Studies
- Phyrex 1.1 - Reconstruction of Continuous Character Trait Values at nodes of Phylogenetic Trees
- PhySamp 1.1.0 - Phylogenetic Sampling and Optimization of Sequence Alignments
- physher v1.0.2 - Phylogenetic Analysis of Genetic data
- PhySIC_IST - Cleaning Source Trees to infer more Informative Supertrees
- phytools 0.7-80 - Phylogenetic Tools in R
- phyutility 2.6 - Phyloinformatic Utility for Trees, Alignments, and Molecular data
- PI 2.0 - Test the Assumption of Phylogenetic Independence
- picante 1.8-2 - R tools for Integrating Phylogenies and Ecology
- PICRUSt2 v2.3.0-b -Phylogenetic Investigation of Communities by Reconstruction of Unobserved States
- PICS-Ord - Extract Phylogeny Information from hard-to-align Regions of Multiple Sequence Alignments
- PIVO 2 - Phylogeny by IteratiVe Optimization
- PLCT 1.0 - Determines Reconciliation Feasibility with Multiple Sampled Individuals and Loci per Species
- PLEX 0.95 - Phylogenetics, Likelihood, Evolution, and CompleXity
- PLL 1.0.2 / libpll-2 0.3.2 - Phylogenetic Likelihood Library
- PluMiST 1.1 - Plus and Minus SuperTrees
- PolyPhy - Microbial Phylogeny Reconstruction with Polytomy Identification
- PolytomySolver 0.1 - Finds an Optimal Binary Resolution of the Gene Tree
- PolytomySolverNAD 0.1 - Polytomy Refinement for the Correction of Dubious Duplications in Gene Trees
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