https://github.com/mitoNGS
https://github.com/HSGU-NIA/mitoAnalyzer
https://github.com/mitoNGS/MToolBox
https://github.com/trichelab/MTseeker
https://bioconductor.org/packages/release/bioc/html/MTseeker.html
https://github.com/Runsheng/mitovar
https://github.com/seppinho/mutation-server Low-Frequency Variant Detection in mtDNA data
https://github.com/mnievesc/Ancient_mtDNA_Pipeline
https://github.com/mrinalmanu/mtDNA-CNV
https://github.com/reenadebray/mtDNA_copy_number
https://github.com/Helgriff/MitoCirco
Online resources for annotation and prioritization of mtDNA variants.
| Tool | Website | References | |
|---|---|---|---|
| A. ANNOTATION TOOLS AND PRIORITIZATION PIPELINES | |||
| MSeqDR MvTool | https://mseqdr.org/ | Shen et al., 2018 | |
| Mitoseek | https://github.com/riverlee/MitoSeek | Guo et al., 2013 | |
| mtDNA-Server | https://mtdna-server.uibk.ac.at/index.html | Weissensteiner et al., 2016a | |
| MITOMASTER | https://www.mitomap.org/foswiki/bin/view/MITOMASTER/WebHome | Lott et al., 2013 | |
| SG-Adviser | https://genomics.scripps.edu/mtdna/ | Rueda and Torkamani, 2017 | |
| Mitotool | http://www.mitotool.org/ | Fan and Yao, 2011 | |
| Mit-O-Matic | http://genome.igib.res.in/mitomatic/help.html | Vellarikkal et al., 2015 | |
| Database | Specificity | Website | References |
| B. ONLINE DATABASES DEDICATED To mtDNA | |||
| HmtDB | mtDNA variants | https://www.hmtdb.uniba.it/ | Clima et al., 2017 |
| HmtVAR | mtDNA variants | https://www.hmtvar.uniba.it/ | Preste et al., 2018 |
| MITOMAP | mtDNA variants | https://www.mitomap.org/foswiki/bin/view/MITOMAP/WebHome | Kogelnik et al., 1996 |
| Mitobreak | mtDNA rearrangements | http://mitobreak.portugene.com | Damas et al., 2014 |
| EMPOP | Forensic database | https://empop.online/ | Parson and Dur, 2007 |
| Mamit-tRNA | tRNA variants | http://mamit-trna.u-strasbg.fr/ | Putz et al., 2007 |
| PhyloTreemt | Phylogenetic tree | http://www.phylotree.org/ | van Oven and Kayser, 2009 |
| Database | Website | References | |
| C. ONLINE GENERAL DATABASES INCLUDING mtDNA DATA | |||
| CLINVAR | https://www.ncbi.nlm.nih.gov/clinvar/ | Landrum et al., 2016 | |
| CLINVAR Miner | https://clinvarminer.genetics.utah.edu/ | Henrie et al., 2018 | |
| OMIM | https://www.omim.org/ | Amberger et al., 2015 | |
| Tool | Specificity | Website | References |
| D. In silico PREDICTION TOOLS | |||
| APOGEE | Coding variants | http://mitimpact.css-mendel.it | Castellana et al., 2017 |
| MToolbox | Coding variants | https://github.com/mitoNGS/MToolBox | Calabrese et al., 2014 |
| Mitimpact2 | Coding variants | http://mitimpact.css-mendel.it/ | Castellana et al., 2015 |
| Mitoclass.1 | Coding variants | https://github.com/tonomartin2/MITOCLASS.1 | Martin-Navarro et al., 2017 |
| MITOTIP | tRNA variants | https://www.mitomap.org/foswiki/bin/view/MITOMAP/MitoTipInfo | Sonney et al., 2017 |
| PON-mt-tRNA | tRNA variants | http://structure.bmc.lu.se/PON-mt-tRNA/ | Niroula and Vihinen, 2016 |
| Haplogrep2 | Haplogroup prediction | https://haplogrep.uibk.ac.at/ | Weissensteiner et al., 2016b |
