List of scripts, small apps and minute software

Here is a short list of a variety of scripts that I coded for biological (or other) uses in diverse programing languages. Also some CSL for citation managers like Mendeley and Zotero. If you want use one of them and have doubts, please contact me by email.

pseudoMiner v.U - 2018
Script to automatice the extraction of information about sequences from GenBank using Entrez database API. Additionally it classifies sequences in categories of kind of study where them were used.
Script in Unique version. Coded in: AutoIt v.3 BASIC-like scripting language
Download source code here

ConvertFileUsingAlterAPI v.1 - 2017
Python script to convert all files in a folder using the API of the webservice of ALTER (Glez-Peña et al. 2010). It can be used in two ways: 1) Paste the file .py in the folder with files to convert and double click it by default it will convert Nexus files to Phylip for using in PhyML. 2) In terminal or cmd in Windows, you can call it using the command line options documented in --help command. If you use this, you must know that it is just a script to execute the ALTER API and you should cited it. Refer to the original ALTER website for more details about citation.
Python script in version 1. Coded in: Python 2.7.11
Download it here

FastChangeNames v.1 - 2017
Change names in files like .tre, .xml, .nexus or others, based on xls file. It performs 1000s changes per second aprox. This script is used to change names in phylogenetic trees files or Nexus matrixes. The input is two columns, one with the current name and the second one is the new name in Excel. This have a graphic interface for easy use.
Script compiled as binary (.exe) in version 1 for Windows 7 or superior. Coded in: AutoIt v.3 BASIC-like scripting language
Download it here for 32bits and here for 64bits

MIC (Manual Image Classify) v.U - 2017
Small application to facilitate the classification or taking data (notes) from images. Saving up to 8 different elements in a *.CSV file like a database.
Script compiled as binary (.exe) in Unique version. Coded in: AutoIt v.3 BASIC-like scripting language
Download it here, source code availible through email request.

HerbivoryScript for ImageJ v.1.2.1 - 2016
Macro to conduct an assisted hervivory area analysis in leaves using images and color threshold functions on ImageJ. This is intended to measure patology and hervivory in leaves, the final result is a table including the percent of the damaged areas. This macro saves photos of the evidence, during the process.
Script in beta version. Coded in: ImageJ Macro Language
Download it here

ChangeNames for Notepad++ v.U - 2014 - deprecated - updated in FastChangeNames script
Change names in files like .tre, .xml, .nexus or others, using Notepad++ to avoid modifications in non-printable characters or other coded characters. It performs 200 changes per minutes aprox. It code is used to change names in phylogenetic trees files or Nexus matrices. The input is two columns, one with the current name and the second one is the new name in Excel.
Script in Unique version. Coded in: AutoIt v.3 BASIC-like scripting language
Download it here

CSL files for different journals
Before you use them, check and double check if this is currently valid for the journal.
CSL for Taxon
CSL for Nomenclature proposals in Taxon
CSL for Systematic botany
CSL for Phytotaxa