|
spread3
|
1:0.9.5-1 |
0 |
0.00
|
a user-friendly application to analyze and visualize pathogen phylodynamic reconstructions resulting from Bayesian inference of sequence and trait evolutionary processes. https://doi.org/10.1093/molbev/msw082 |
malacology
|
2023-04-28 05:27 (UTC) |
|
spread
|
1.0.7-6 |
0 |
0.00
|
a user-friendly application to analyze and visualize phylogeographic reconstructions resulting from Bayesian inference of spatio-temporal diffusion. https://doi.org/10.1093/bioinformatics/btr481 |
malacology
|
2023-05-06 15:46 (UTC) |
|
spa
|
2014.03.10-0 |
0 |
0.00
|
Sankoff Parsimony Analysis https://doi.org/10.1006/clad.1998.0068 |
malacology
|
2023-07-29 17:57 (UTC) |
|
soapnuke
|
2.1.9-1 |
0 |
0.00
|
A Tool for integrated Quality Control and Preprocessing on FASTQ or BAM/CRAM files http://dx.doi.org/10.5524/100361 |
malacology
|
2024-03-28 18:01 (UTC) |
|
slf-wt
|
2014.03.10-0 |
0 |
0.00
|
A prototype program implementing character state reconstructions under non-lineal functions of the state changes (Pee-Wee with SeLF-WeighTed) https://doi.org/10.1006/clad.1997.0043 |
malacology
|
2023-07-29 17:57 (UTC) |
|
sfa-spa
|
0.2.1-0 |
0 |
0.00
|
A short peptide assembler for metagenomic data https://doi.org/10.1093/nar/gkt118 |
malacology
|
2023-03-04 19:13 (UTC) |
|
seqan3
|
3.3.0-1 |
0 |
0.00
|
The modern C++ library for sequence analysis https://doi.org/10.1016/j.jbiotec.2017.07.017 |
malacology
|
2023-10-06 15:14 (UTC) |
|
seaview
|
5.0.5-8 |
11 |
0.00
|
GUI for multiple sequence alignment and molecular phylogeny. https://doi.org/10.1093/molbev/msp259 |
malacology
|
2022-09-03 01:59 (UTC) |
|
revbayes-mpi
|
1.2.2-1 |
1 |
0.00
|
Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language https://doi.org/10.1093/sysbio/syw021 |
malacology
|
2023-06-10 05:23 (UTC) |
|
revbayes
|
1.2.2-1 |
1 |
0.00
|
Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language https://doi.org/10.1093/sysbio/syw021 |
malacology
|
2023-06-10 05:44 (UTC) |
|
raxmlgui
|
2.0.10-2 |
1 |
0.00
|
A new user-friendly program integrating RAxML-NG and ModelTest-NG for cutting-edge phylogenetic analysis. https://doi.org/10.1111/2041-210X.13512 |
malacology
|
2023-12-05 00:03 (UTC) |
|
raxml-ng-mpi
|
1.2.1-1 |
0 |
0.00
|
A phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion. https://doi.org/10.1093/bioinformatics/btz305 |
malacology
|
2023-12-22 18:14 (UTC) |
|
raxml-ng
|
1.2.1-1 |
1 |
0.00
|
A phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion. https://doi.org/10.1093/bioinformatics/btz305 |
malacology
|
2023-12-22 18:11 (UTC) |
|
raxml-light
|
1.0.9-1 |
0 |
0.00
|
A tool for computing terabyte phylogenies https://doi.org/10.1093/bioinformatics/bts309 |
malacology
|
2022-08-29 01:53 (UTC) |
|
popart
|
2019.07.15-6 |
0 |
0.00
|
Full-feature software for haplotype network reconstruction. https://doi.org/10.1111/2041-210X.12410 |
malacology
|
2023-07-02 18:33 (UTC) |
|
pibuss
|
1.10.4-0 |
1 |
0.00
|
a BEAST/BEAGLE utility for sequence simulation, which provides an easy to use interface that allows flexible and extensible phylogenetic data fabrication. https://doi.org/10.1186/1471-2105-15-133 |
malacology
|
2023-05-07 11:21 (UTC) |
|
phylosuite
|
1.2.3-2 |
0 |
0.00
|
an integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies. https://doi.org/10.1111/1755-0998.13096 |
malacology
|
2023-04-04 19:09 (UTC) |
|
phylonet
|
3.8.4-3 |
0 |
0.00
|
suite of software tools for reconstructing/analyzing phylogenetic networks in the presence of reticulate evolutionary events. https://doi.org/10.1093/sysbio/syy015 |
malacology
|
2022-12-01 18:01 (UTC) |
|
phylogeography
|
1.10.4-0 |
1 |
0.00
|
BEAST PhyloGeography https://doi.org/10.1186/1471-2148-7-214 |
malacology
|
2023-05-07 11:21 (UTC) |
|
phylobayes-mpi
|
1.9-1 |
1 |
0.00
|
phylogenetic reconstruction using infinite mixtures. https://doi.org/10.1093/molbev/msh112 |
malacology
|
2022-10-16 08:44 (UTC) |
|
phast-win
|
2014.03.10-0 |
0 |
0.00
|
PHylogenetic Analysis for Sankoff Transformations https://doi.org/10.1006/clad.1998.0068 |
malacology
|
2023-07-29 17:57 (UTC) |
|
pamlx
|
1.3.1-4 |
0 |
0.00
|
A Graphical User Interface for PAML https://doi.org/10.1093/molbev/mst179 |
malacology
|
2024-02-05 17:10 (UTC) |
|
paml
|
4.10.7-1 |
0 |
0.00
|
Phylogenetic analysis by maximum likelihood. https://doi.org/10.1093/molbev/msm088 |
malacology
|
2023-06-29 22:48 (UTC) |
|
oblong
|
2014.03.10-1 |
0 |
0.00
|
A program to analyse phylogenomic data sets with millions of characters, requiring negligible amounts of RAM. https://doi.org/10.1111/cla.12056 |
malacology
|
2022-08-29 19:55 (UTC) |
|
mrbayes-mpi-beagle
|
3.2.7-15 |
0 |
0.00
|
MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. https://doi.org/10.1093/sysbio/sys029 |
malacology
|
2022-08-02 18:13 (UTC) |
|
mrbayes-mpi
|
3.2.7-8 |
2 |
0.00
|
MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. https://doi.org/10.1093/sysbio/sys029 |
malacology
|
2022-08-02 12:01 (UTC) |
|
mrbayes-beagle
|
3.2.7-6 |
0 |
0.00
|
A program for the Bayesian estimation of phylogeny. https://doi.org/10.1093/sysbio/sys029 |
malacology
|
2022-04-23 18:37 (UTC) |
|
mptp
|
0.2.5-1 |
0 |
0.00
|
A tool for single-locus species delimitation https://doi.org/10.1093/bioinformatics/btx025 |
malacology
|
2023-09-13 00:01 (UTC) |
|
mpi-bucky
|
1.4.4-2 |
0 |
0.00
|
Bayesian Untangling of Concordance Knots https://doi.org/10.1093/bioinformatics/btq539 |
malacology
|
2022-08-29 18:58 (UTC) |
|
mpboot
|
1.2-1 |
0 |
0.00
|
Fast phylogenetic maximum parsimony tree inference and bootstrap approximation https://doi.org/10.1186/s12862-018-1131-3 |
malacology
|
2023-02-14 12:03 (UTC) |
|
morphoj
|
1.08.01-2 |
1 |
0.00
|
integrated program package for doing geometric morphometrics https://doi.org/10.1111/j.1755-0998.2010.02924.x |
malacology
|
2023-10-26 06:07 (UTC) |
|
modeltest-ng-mpi
|
0.1.7-7 |
0 |
0.00
|
A New and Scalable Tool for the Selection of DNA and Protein Evolutionary Models. https://doi.org/10.1093/molbev/msz189 |
malacology
|
2022-08-28 22:03 (UTC) |
|
modeltest-ng
|
0.1.7-6 |
0 |
0.00
|
A New and Scalable Tool for the Selection of DNA and Protein Evolutionary Models. https://doi.org/10.1093/molbev/msz189 |
malacology
|
2023-03-25 22:23 (UTC) |
|
modeltest-gui
|
0.1.7-8 |
0 |
0.00
|
A New and Scalable Tool for the Selection of DNA and Protein Evolutionary Models. https://doi.org/10.1093/molbev/msz189 |
malacology
|
2022-08-28 22:03 (UTC) |
|
mega
|
11.0.13-3 |
1 |
0.00
|
Molecular Evolutionary Genetics Analysis. https://doi.org/10.1093/molbev/msy096 |
malacology
|
2023-04-04 19:30 (UTC) |
|
mcscanx
|
2022.11.01-1 |
0 |
0.00
|
Multiple Collinearity Scan toolkit X version https://doi.org/10.1093/nar/gkr1293 |
malacology
|
2023-02-09 11:42 (UTC) |
|
lvb
|
4.2-0 |
0 |
0.00
|
parsimony and simulated annealing in the search for phylogenetic trees https://doi.org/10.1093/bioinformatics/btg402 |
malacology
|
2023-07-29 12:26 (UTC) |
|
last
|
1543-1 |
0 |
0.00
|
Genomic aligner for short reads https://doi.org/10.1093/nar/gkq010 |
malacology
|
2024-04-15 12:01 (UTC) |
|
jmodeltest
|
2.1.10r20160303-7 |
1 |
0.00
|
Phylogenetic Model Averaging, more models, new heuristics and high-performance computing. https://doi.org/10.1093/molbev/msn083 |
malacology
|
2022-08-29 21:04 (UTC) |
|
jml
|
1.3.1-2 |
0 |
0.00
|
Testing hybridization using species trees https://doi.org/10.1111/j.1755-0998.2011.03065.x |
malacology
|
2022-08-28 10:37 (UTC) |
|
jane
|
4.01-5 |
0 |
0.00
|
software tool for the cophylogeny reconstruction problem. https://doi.org/10.1186/1748-7188-5-16 |
malacology
|
2022-12-01 12:01 (UTC) |
|
iqtree-mpi
|
2.3.2-1 |
0 |
0.00
|
Efficient phylogenomic software by maximum likelihood; multicore version (OMP). https://doi.org/10.1093/molbev/msaa015 |
malacology
|
2024-04-11 12:05 (UTC) |
|
iqtree
|
2.3.2-1 |
2 |
0.00
|
Efficient phylogenomic software by maximum likelihood https://doi.org/10.1093/molbev/msaa015 |
malacology
|
2024-04-11 12:11 (UTC) |
|
hybpiper
|
2.1.6-1 |
0 |
0.00
|
Recovering genes from targeted sequence capture data https://doi.org/10.3732/apps.1600016 |
malacology
|
2024-02-13 09:49 (UTC) |
|
generax
|
2.1.3-1 |
0 |
0.00
|
A Tool for Species-Tree-Aware Maximum Likelihood-Based Gene Family Tree Inference under Gene Duplication, Transfer, and Loss https://doi.org/10.1093/molbev/msaa141 |
malacology
|
2024-01-16 20:30 (UTC) |
|
gblocks
|
0.91b-7 |
1 |
0.00
|
A program written in ANSI C language that eliminates poorly aligned positions and divergent regions of an alignment of DNA or protein sequences. https://doi.org/10.1093/oxfordjournals.molbev.a026334 |
malacology
|
2024-01-18 12:01 (UTC) |
|
gatk
|
4.5.0.0-1 |
1 |
0.00
|
Genome Analysis Toolkit https://doi.org/10.1101/gr.107524.110 |
malacology
|
2023-12-14 00:08 (UTC) |
|
fastuniq
|
1.1-1 |
0 |
0.00
|
ultrafast de novo tool for removal of duplicates in paired short DNA sequence reads in FASTQ format https://doi.org/10.1371/journal.pone.0052249 |
malacology
|
2024-02-14 18:01 (UTC) |
|
fastme
|
2.1.6.3-1 |
0 |
0.00
|
a comprehensive, accurate and fast distance-based phylogeny inference program https://doi.org/10.1093/molbev/msv150 |
malacology
|
2023-10-11 09:46 (UTC) |
|
fastdnaml
|
1.2.2-0 |
0 |
0.00
|
A tool for construction of phylogenetic trees of DNA sequences using maximum likelihood https://doi.org/10.1093/bioinformatics/10.1.41 |
malacology
|
2024-02-05 02:14 (UTC) |