Links



Download iTaxoTools



iTaxoTools is a diversified collection of tools for integrative taxonomy, with the goal of providing user-friendly access to their function via user-friendly graphical interfaces.

All tools are available as stand-alone Windows executables. We also provide links to the respective source codes (almost all on GitHub).

For selected tools we provide executables also for Apple Macintosh platforms.

We assume that most researchers familiar with Linux will prefer running the tools directly from the source code, but Linux executables for most tools are also provided (as batch download at the end of this page).

Unless specified otherwise, the tools are in the initial alpha-version (0.1), but will be consecutively replaced with more advanced versions.

The following table provides download links for all single tools. At the end of this webpage there are links for the entire package of tools, the manual, and example files.



Download single Modules


Molecular data preparation

Windows executable

Source code

DNAconvert: Converts among DNA sequence formats
- Supports typical sequence formats (fasta, fastq, phylip, nexus)
- Autocorrects typical errors in sequence files such as non-standard characters in sequence names.
- Reads GenBank flat files and converts from and to tab-delimited files to manage sequences in spreadsheet editors.
- Single-file conversion, batch conversion and conversion of copy-pasted files
Windows executable

Source code

Fastmerge: Merges DNA sequence files (fasta, fastq)
- Can merge large files that usually cannot be opened in editors.
- Works for any text file but includes additional features when processing fasta and fastq.
- Allows for filtering sequences and sequence names with certain motifs and to include/exclude them in the merged file
Windows executable

Source code

Fastsplit: Splits (large) DNA sequence files (fasta, fastq) into smaller files
- Can split large files of several GB in size that usually cannot be opened in editors into a series of equally sized smaller files
- Designed for fasta and fastq, but works for any text file.
- Allows for filtering sequences and sequence names with certain motifs and to include/exclude them in the split files
Windows executable

Source code

PyR8S: Calculates ultrametric timetrees (chronograms) based on non-parametric rate-smoothing
- Takes as input treefiles with branch length (phylograms)
- Transforms into ultrametric using non-parametric rate smoothing, without the need to access original data (sequences)
- User-friendly interface to set time constraints (calibrations) on nodes.
Windows executable

Mac executable

Source code

Manual / tutorial appendix

Example files

Concatenator: Concatenates sequences of different markers based on sample name

NEW TOOL

- Handles multiple input format, including tab-delimited files
- Extremely user-friendly and intuitive interface
- Includes MAFFT for (re)aligning single markers
- Includes option for fast calculation of gene trees using FastTree
- Includes options for output validation

Windows executable

Mac executable

Source code

Manual / tutorial appendix

Original program

MAFFT: Fast and reliable sequence alignment

NEW TOOL

- A Python-based GUI for the popular alignment program MAFFT
- Implements two alignment strategies of the original program (FFT-NS-1 and G-INS-i)

Windows executable

Mac executable

Source code

Manual / tutorial appendix

Original program

FastTree: Fast inference of approximately-maximum-likelihood phylogenetic trees

NEW TOOL

- A Python-based GUI for FastTree
- Fast inference of approximately-maximum-likelihood phylogenetic trees from large alignments with many taxa

Windows executable

Source code

Nodenamecorrector: Removes special characters from terminal node names in Newick-formatted trees
- Takes as input a Newick treefile, identifies node names, searches for characters in node names that are not standard alphanumerical, and replaces them with underscores


Data analysis: diagnosis
Windows executable

Source code

DNAdiagnoser: Computes diagnostic sites for species from DNA sequences
- Takes as input aligned or unaligned sequence files in fasta or tab-delimited text format
- Unaligned sequences are pairwise aligned to reference sequence and differences recorded relative to position in reference
- Summarizes variation within species and outputs diagnostic sites among species
- Outputs unique diagnostic sites for the whole data sets, as well as diagnostic sites in pairwise comparisons among species
- Output is given in the form of tables but also as text which can be used for species diagnoses in taxonomic papers
Windows executable

Source code

TaxI2: Calculates inter- and intraspecific distances and the barcoding gap based on pairwise-aligning DNA sequences
- Takes as input aligned or unaligned sequence files in fasta or tab-delimited text format
- For unaligned sequences, pairwise alignments are performed
- Calculates pairwise genetic distances among all sequences
- If tab file contains row with species names, inter- and intra-species distances are calculated and summarized, and the barcoding gap as well as some summary statistics of the barcoding gap calculated
- Inter-species distances are calculated separately for species of the same genus vs. different genera
- A histogram illustrating the barcoding gap is produced in editable PDF format
Windows executable

Source code (iTT GUI)

Source code (original program)

MolD: Recovers DNA-based diagnoses for taxa from DNA sequence alignments
- Implements MolD with a Python-based GUI
- Recovers diagnostic combinations of nucleotides (DNCs) for pre-defined groups of DNA sequences, corresponding to taxa
- Identifies pure diagnostic sites, minimal DNCs (mDNCs), and redundant DNCs (rDNCs), the latter fulfil predefined criteria of reliability


Data analysis: delimitation
Windows executable

Source code (iTT GUI)

Source code (original program)

ASAP: Species delimitation from single-locus sequence data by the Assemble Species by Automatic Partitioning approach
- Implements ASAP with a Python-based GUI
- Takes as input a set of aligned sequences and calculates pairwise distances
- Proposes species partitions ranked by a new scoring system that uses no biological prior insight of intraspecific diversity.
Windows executable

Source code (iTT GUI)

Source code (original program)

ABGD: Species delimitation by automatic barcoding gap discovery
- Implements ABGD with a Python-based GUI
- Takes as input a set of aligned sequences and calculates pairwise distances
- Uses a coalescent model to identify the position of the most likely barcode gap, based on a maximal genetic intraspecific divergence defined a priori by the user.
- Uses the DNA barcoding gap to propose species partitions.
Windows executable

Source code (iTT GUI)

Source code (original program)

DELINEATE: Species delimitation by integrating an explicit model of speciation into the multipopulation coalescent
- Implements DELINEATE with a Python-based GUI
- Takes as input a rooted ultrametric tree from a multispecies coalescent analysis, in Nexus or Newick format
- Second input file is a table assigning specimens to species, or flagging their species identity as unknown
- Outputs various alternative species partitions, ranked by probability
Windows executable

Source code (iTT GUI)

Source code (original program)

GMYC: Species delimitation based on the Generalized Mixed Yule Coalescent
- Implements GMYC with a Python-based GUI
- Uses as input an ultrametric tree in Newick or Nexus format
- Uses a likelihood approach to analyze the timing of branching events, seeking for significant switches between a Yule (interspecific) and a coalescent (intraspecific) branching structure.
Windows executable

Source code (iTT GUI)

Source code (original program)

PTP: Species delimitation based on Poisson tree processes
- Implements PTP with a Python-based GUI
- Uses as input a non-ultrametric tree with branch lengths (phylogram) in Newick or Nexus format
- Models speciation on branching events in terms of number of mutations (inferred from branch lengths)
- Bayesian and ML versions of PTP are implemented
Windows executable

Source code (iTT GUI)

Source code (original program)

TR2: Species delimitation using Bayesian model comparison and rooted triplets
- Implements TR2 with a Python-based GUI
- Takes as input a set of gene trees, and optionally a guide species tree
- Calculates posterior probability scores for user-specified delimitation hypotheses.
- Alternatively, finds the best delimitation under a guide tree specifying a hierarchical structure of species grouping.
Windows executable

Source code

Morphometricanalyzer: Calculates a series of basic statistical comparisons of species based on morphometric data
- Takes as input tab-delimited files with morphometric measurements
- Calculates summary statistics, pairwise comparisons (t-tests, U-tests), ANOVAs, etc
- Size-corrects values by calculating ratio against a reference measurement such as body size
- Writes text output summarizing diagnostic characters (scientifically different measurements between species, with and without overlap of ranges)

Data preparation
Windows executable

Source code

Simplestatscalculator: Performs a series of basic statistical analyses
- Values are typed or pasted into text boxes
- Descriptive statistics (mean, median, standard deviation, and others)
- Pairwise comparisons (t-test, U-test)
- Comparisons of distributions (Chi-square, normality, Fisher’s)
- Corrections for multiple testing
Windows executable

Source code

Specimentablemerger: Merges data from two tables based on values in the row “specimen”
- Takes as input two or more tab-delimited files, compares values in column “specimen” (or other chosen
column) and merges into one table, combining values for same specimen number in the same row
- Automatically checks for duplicate values of the same variable and specimen and issues warnings
Windows executable

Source code

Specimentablepruner: Removes rows from tables based on a list of
values for the row “specimen”
- Takes as input a tab-delimited file and a series of values of specimen identifiers
- Removes all rows from the table where the column “specimen” (or other chosen column) agrees with any of the provided values
Windows executable

Source code

Latlonconverter: Converts among different geographic coordinate formats
- Parses a large variety of formats of WGS84 geographical coordinates
- Batch-conversion of coordinates in tables or copy-pasted lists which can contain coordinates in different
formats (recognized by heuristic approach)
- Main output in decimal degree format
Windows executable

Source code

Linebreaker: Changes among line break formats (Unix, Windows, Mac)
- Takes as input any text file and changes all line breaks to the specified format
Windows executable

Source code

Unitconverter: Converts among different units
- Values are typed into one field, all other fields show converted values in real time
- Separate tabs for conversion of distance, volume, time, molarity, and others


Data integration
Windows executable

Source code

SPARTmapper: Computes a kml file from geographical coordinates and spart file
- Takes as input a text file with decimal geographical coordinates and specimen identifiers, and a species partition (SPART) file
- Outputs a kml file to show localities by species on Google Earth
Windows executable

Source code

Limes: Compares species partitions and parses/merges/exports SPART files
- Reads species partition (SPART) files, as well as species partition information in spreadsheet format
- Computes Ctax,mCtax,Rtax and Match Ratio indexes
- Can merge, extract and export SPART files

Download the full package of iTaxoTools 0.1 as of June 2021:

Download the launcher
(a single executable that includes all tools developed by June 2021; so far only available for Windows)




Download the full package
(the most comprehensive version: a compressed folder including executables for all single tools, the manual in PDF format, example files for all tools, and in the Windows version also the launcher)
Note: both the Windows and Linux versions are large files, of more than 2-3 GB.



Download the iTaxotools manual

Download the manual appendix for Concatenator, MAFFT and FastTree


Download the package of example files (ZIP folder)
(a complete set of example files for all tools)




Copyright notice / contact: Website maintained by M. Vences
(institutional address: Zoological Institute, TU Braunschweig, Mendelssohnstr. 4, 38106 Braunschweig, Germany)