Useful Links

My work on Heterotheca relies upon a wide variety of programs and software. These tools are a mixture of GUIs and direct programming, and note that certain resources below require subscriptions to use.

Recommended Resources:

AliView (https://github.com/AliView/AliView): view individual gene trees and modify alignments, ex. remove gap-only sites

ArcGIS Pro (https://www.esri.com/en-us/arcgis/products/arcgis-pro/overview): generate a wide variety of maps through ESRI’s software (requires subscription for any usage)

ASTRAL (https://github.com/smirarab/ASTRAL): produce coalescent trees from sets of gene trees

BEAST2 (https://www.beast2.org/): estimate ultrametric/time-calibrated phylogenetic trees under a Bayesian framework

BioClim (https://www.worldclim.org/data/index.html): access global climatic/environmental data such as precipitation and temperature

BioGeoBEARS (https://github.com/nmatzke/BioGeoBEARS): ancestral state reconstruction of ultrametric trees, especially for biogeographic areas

FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/): evaluate the quality of sequence reads

FastTree (https://github.com/morgannprice/fasttree): generate ultrafast maximum likelihood phylogenies

FigTree (https://tree.bio.ed.ac.uk/software/figtree/): view and rearrange phylogenetic trees

Geneious Prime (https://www.geneious.com/): view multiple sequence alignments, build gene trees, convert between file formats and much, much more (subscription required for most features)

HybPhaser (https://github.com/LarsNauheimer/HybPhaser): modify HybSeq/target-capture sequence data to account for polymorphisms and filter out data based on multiple factors

HybPiper (https://github.com/mossmatters/HybPiper): assemble and collateHybSeq/target-capture sequence data

ImageJ (https://imagej.net/ij/): measure images of herbarium specimens which have a calibration reference (ex. a ruler)

IQ-TREE (https://iqtree.github.io/): generate maximum likelihood phylogenies and estimateconcordance concordance factors principally

MAFFT (https://mafft.cbrc.jp/alignment/server/index.html): generate rapid multiple sequence alignments

MaxEnt (https://biodiversityinformatics.amnh.org/open_source/maxent/): the primary software used in generating ecological niche models

MrBayes (https://nbisweden.github.io/MrBayes/): produce Bayesian Inference phylogenies

Orthofinder (https://github.com/davidemms/OrthoFinder): reformat HybSeq/target-capture sequence data to filter out paralogs in an amino acid format

PAUP (https://paup.phylosolutions.com/): calculate proportions of invariant sites, estimate optimal site models, produce parsimony trees, and more

Phyparts (https://github.com/mossmatters/MJPythonNotebooks): estimate concordance and discordance among sets of gene trees

QGIS (https://qgis.org/download/): generate a wide variety of maps with a similar to GUI to ArcMap before it was discontinued

R/R Studio (https://cran.r-project.org/): write code for an enormous variety of uses, including morphometrics, phylogenetics, map-making, and much, much more

RAxML (https://github.com/amkozlov/raxml-ng): generate maximum likelihood phylogenies

SDMToolBox (http://www.sdmtoolbox.org/downloads): useful for a wide variety of spatial functions including ecological niche modeling

Seaview (https://bio.tools/seaview): view individual gene trees

SoilGrids (https://www.soilgrids.org/): access global soil data

Spruceup (https://github.com/marekborowiec/spruceup): trim divergent sequences from multiple sequence alignments

Tracer (https://tree.bio.ed.ac.uk/software/tracer/): view the output of Bayesian Inference methods (ex. BEAST2 and MrBayes)

Treeshrink (https://github.com/uym2/TreeShrink): prune aberrantly long branches from gene trees

trimAl (https://github.com/inab/trimal): truncate ends of multiple sequence alignments with low coverage

trimmomatic (https://github.com/usadellab/Trimmomatic): remove adapters and low-quality portions of sequence reads