Bioinformatics & Software

I am a passionate user of computer software and internet platforms, especially in the fields of bioinformatics and phylogenetics. Here is a list of software that you may also find useful in your own work. Many thanks to everyone that supports free and open-source software.

Software in bioinformatics

ANCHOR: A 16S rRNA gene amplicon pipeline for microbial analysis of multiple environmental samples.

BEAST http://beast.bio.ed.ac.uk/Main_Page

BEAUTi http://beast.bio.ed.ac.uk/BEAUti

Bioconductor https://www.bioconductor.org/

BioEdit http://www.mbio.ncsu.edu/bioedit/bioedit.html

Biorender: https://biorender.com/

Calour: an Interactive, Microbe-Centric Analysis Tool https://github.com/biocore/calour. More information here.

CIRCOS: http://circos.ca/software/download/

CLC Sequence Viewer http://www.clcbio.com/products/clc-sequence-viewer/

Clustal http://www.clustal.org/

Cytoscape http://www.cytoscape.org/

Environmental Omics link to Bio-Linux http://environmentalomics.org/bio-linux/

ESPRIT http://www.ijbcb.org/ESPRITPIPE/php/onlinetool.php

FigTree http://tree.bio.ed.ac.uk/software/figtree/

GeneDoc (http://www.nrbsc.org/gfx/genedoc/

GitHub https://github.com/

Huttenhower lab Galaxy server: https://huttenhower.sph.harvard.edu/galaxy/

ImageJ http://rsb.info.nih.gov/ij/index.html

MetaPhlAn 2: Metagenomic Phylogenetic Analysis

MicrobiomeAnalyst (associated paper)

Mothur http://www.mothur.org/

mPUMA microbial Profiling Using Metagenomic Assembly http://mpuma.sourceforge.net/

MrBayes http://mrbayes.sourceforge.net/

MUSCLE http://www.drive5.com/muscle/

PHYLIP http://evolution.genetics.washington.edu/phylip.html

pyseer https://github.com/mgalardini/pyseer

QIIME http://qiime.org/

And of course QIIME2!!

SplitsTree http://www.splitstree.org/

STAMP http://kiwi.cs.dal.ca/Software/STAMP

TreeView http://taxonomy.zoology.gla.ac.uk/rod/treeview.html

UMAP (Uniform Manifold Approximation and Projection for Dimension Reduction) Reference.

UniFrac http://bmf2.colorado.edu/unifrac/about.psp

Unipro UGENE http://ugene.unipro.ru/

Scilab http://www.scilab.org/en/scilab/about

SigTree https://cran.r-project.org/web/packages/SigTree/index.html

STITCH https://www.ncbi.nlm.nih.gov/pubmed/21113709

metaBEETL https://github.com/BEETL/BEETL

PICRUSt http://galaxy.morganlangille.com/

Piphilin http://www.secondgenome.com/solutions/resources/data-analysis-tools/piphillin/

Python for Biologists https://pythonforbiologists.com/

PseudoMLSA Database http://microbiologia.uib.es/bioinformatica/Welcome.html

Interactive Tree of Life https://itol.embl.de/

FLASH: fast length adjustment of short reads to improve genome assemblies http://ccb.jhu.edu/software/FLASH/

iMAP: an integrated bioinformatics and visualization pipeline for microbiome data analysis (paper)

Introducing SONS, a Tool for Operational Taxonomic Unit-Based Comparisons of Microbial Community Memberships and Structures.

Draw Venn Diagram http://bioinformatics.psb.ugent.be/webtools/Venn/

Internet platforms

BugBase https://bugbase.cs.umn.edu/

FINDMODEL and other cool tools http://www.hiv.lanl.gov/content/sequence/HIV/HIVTools.html

PanFP: pangenome-based functional profiles for microbial communities https://github.com/srjun/PanFP

PICRUSt http://picrust.github.io/picrust/

Tax4Fun http://www.ncbi.nlm.nih.gov/pubmed/25957349

OMIA Online Mendelian Inheritance in Animals http://omia.angis.org.au/home/

Molecular Revolution http://www.molecularevolution.org/

The Aspergillus website http://www.aspergillus.org.uk/

MicrobeWiki https://microbewiki.kenyon.edu/index.php/MicrobeWiki Amazing collection of very cool things about microbes

Very interesting and informative map of cases of melioidosis worldwide http://www.melioidosis.info/map.aspx

MetaCoMET: a web platform for discovery and visualization of the core microbiome.

COREMIC: a web-tool to search for a niche associated CORE MICrobiome.

Reverse Complement. This tool made me think a lot, it converts a DNA sequence into its reverse, complement, or reverse-complement counterpart. During the analysis of data from Dr. Cuauhtemoc Licona, I noticed (for the first time) the following message from Mothur after aligning with align.seqs:

"Some of you sequences generated alignments that eliminated too many bases, a list is provided in sequences.flip.accnos. If you set the flip parameter to true mothur will try aligning the reverse compliment as well."

Statistics

R http://www.r-project.org/

SAS and JMP http://www.sas.com/

There is a new free SAS version http://www.sas.com/en_us/software/university-edition.html

I found this with lots of information and many useful lectures about statistics from Penn State.

Programming

Python http://www.python.org/

Scratch http://scratch.mit.edu/

Databases

RNA Databases

1. Noncoding RNA database http://biobases.ibch.poznan.pl/ncRNA/

This website is very useful because it contains links to other RNA databases

BLAST is not working

2. miRBase: the microRNA database http://www.mirbase.org/

Very useful and functional (April 27, 2016)

3. Bacterial small regulatory RNA database www.bac-srna.org/

The website is not functional so in case you need it here is the paper. For myself: this is the BEST for RDP project

4. sRNAdb: A small non-coding RNA database for gram-positive bacteria http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-13-384

This is another one but for gram-positive bacteria only. Also not functional :(

5. A comprehensive database of bacterial sRNA targets verified by experiments sRNATarBase http://ccb.bmi.ac.cn/srnatarbase/

Fortunately several groups of researchers are investigating this and other cool things about sRNAs (for example the Polacek group)

Other databases

The MIT/ICBP siRNA database http://web.mit.edu/sirna/

BAliBASE http://www-bio3d-igbmc.u-strasbg.fr/balibase/

DNA Data Bank of Japan http://www.ddbj.nig.ac.jp/

European Molecular Biology Laboratory http://www.embl.de/

GreenGenes http://greengenes.lbl.gov/cgi-bin/nph-index.cgi

National Center for Biotechnology Information http://www.ncbi.nlm.nih.gov/

Ribosomal Database Project http://rdp.cme.msu.edu/

SILVA https://www.arb-silva.de/

Saccharomyces Genome Database http://www.yeastgenome.org/

CyanoDB A Database of Cyanobacterial genera http://www.cyanodb.cz/

Human Oral Microbiome Database http://www.homd.org/

The chaperonin database http://www.cpndb.ca/

****The Ribosomal RNA Database https://rrndb.umms.med.umich.edu/****

Labome http://www.labome.org/. At first you get the Journal Research and there seems to be nothing else. However, type the name of a bacterial group (Burkholderiaceae) and you will be happy.

The Bovine Genome Database http://bovinegenome.org/

FAOSTAT http://www.fao.org/faostat/en/

Microbial compendium http://www.microbialcompendium.com/

Accumulating the Fungal Tree of Life http://aftol.org/

Servicio de Informacion Agroalimentaria y Pesquera https://www.gob.mx/siap/

List of prokaryotic names with standing in nomenclature http://www.bacterio.net/index.html

Leading International Fungal Education http://www.life-worldwide.org/

R packages

microbiome R package.

phyloseq. Associated paper.

metamicrobiomeR. Associated paper.

Other tools

Nucleotide substitutions models http://www.molecularevolution.org/resources/models/nucleotide

Home of the glycemic index http://www.glycemicindex.com/index.php

Phenol explorer http://phenol-explorer.eu/

Training in Bioinformatics

EVOLUTION AND GENOMICS. Intensive and comprehensive training workshops.

An Introduction to Applied Bioinformatics by Greg Caporaso http://readiab.org/

Cool places and laboratories around the world

Microbiology is for sharing! By Dr. Suzanne L. Ishaq.

Dr. Mizrahi's lab is so cool that I thought I had to share it enjoy.

Centro de Referencia para Lactobacilos en Argentina.

Micropia is a museum in Amsterdam based on the idea of distributing information about microbes, which are often associated with illness and disease despite their essential function in the daily functioning of human life. The museum opened on 30 September 2014 and it claims to be the first of its kind.

Microbiosymas http://www.microbiosymas.com/index.html

Unidad Universitaria de Secuenciacion Masiva y Bioinformatica, UNAM http://uusmd.unam.mx/

The Beef Cattle Institute https://www.beefcattleinstitute.org/publications/

Gut Bacteriology Research Group (Mills Lab)

Other random stuff

Table 1 in this paper written by Andrey N. Shkoporov and Colin Hill shows several software tools and databases useful in phage and viral metagenomic analysis.

One of the best descriptions of phylogenetics (link)

Download videos using savefrom http://es.savefrom.net/. And to get the audio only https://online-audio-converter.com/

Convert PDF into high-quality jpg files https://pdf2jpg.net/

Screen Recorder and other ways to record your screen in Windows 7 http://www.wikihow.com/Record-Screen-in-Microsoft-Windows-7

Cool resources in Microbial Ecology http://www.microbial-ecology.net/