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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

Current version: DNAconvert 1.0 [February 2023]

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

Current version: Fastmerge 0.1 [August 2021]

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

Current version: Fastsplit 0.1 [August 2021]

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.

Current version: Pyr8s 0.1 [August 2021]

MAFFTpy: Fast and reliable sequence alignment

• 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)

Current version: MAFFTpy 0.1 [May 2022]

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

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

Current version: FastTreePy 0.1 [May 2022]

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

Current version: Nodenamecorrector 0.1 [August 2021]

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

Current version: MolD 1.4.1 [completely reworked GUI version, June 2023]

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/li>
• 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
• Update: Most features of DNAdiagnoser have been included in MolD, version 1.4.1, as of June 2023. We recommend using MolD for molecular diagnoses.

Current version: DNAdiagnoser 0.1 [August 2021]

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.

Current version: ABGDpy 0.1 [August 2021]

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

Current version: PTP-pyqt5 0.1 [August 2021]

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.

Current version: GMYC-pyqt5 0.1 [August 2021]

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.

Current version: TR2-pyqt5 0.1 [August 2021]

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

Current version: DELINEATE-pyqt5 0.1 [August 2021]

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)

Current version: Morphometricanalyzer 0.1 [August 2021]

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

Current version: Simplestatscalculator 0.1 [August 2021]

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

Current version: Specimentablemerger 0.1 [August 2021]

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

Current version: Specimentablepruner 0.1 [August 2021]

Linebreaker: Changes among line break formats (Unix, Windows, Mac)

• Takes as input any text file and changes all line breaks to the specified format

Current version: Linebreaker 0.1 [August 2021]

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

Current version: Unitconverter 0.1 [August 2021]

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

Current version: LIMES 2.0 [August 2021]

Decontaminator: Runs a variety of scripts to remove potential paralogs/contaminants from phylogenomic data sets

• Experimental alpha version, untested and not optimized for user-friendliness.

Referenceformatter: Adjusts format in reference lists

• Experimental alpha version, not optimized for user-friendliness. This program can be very useful to re-format extensive reference lists but may introduce errors with complex reference formats (book chapters) or complex author names (e.g., compound surnames).

SequenceChecker: Provides basic information and statistics on DNA sequences in fasta files (and other formats)

• Experimental alpha version, not optimized for user-friendliness but probably without major bugs.

SpartParser: Checks and converts between Spart and SpartXML files

• Experimental alpha version, not optimized for user-friendliness but working reliably.

ConvPhase: Convenient phasing of heterozygous DNA sequences

• Experimental alpha version, fully functional.

Hapsolutely: Phasing, haplotype networks, Fitch genealogies, Fields of recombination

• Experimental alpha version, fully functional.