Name | Alignment to | Transcript information | Year of release | Link | Pubmed Id |
BitSeq | Transcriptome | Sequences | 2012 | http://bitseq.github.io/ | 24413218, 22563066 |
CEM | Genome | Annotations | 2012 | http://alumni.cs.ucr.edu/~liw/cem.html | 23060617 |
Cufflinks | Genome | Annotations | 2010 | http://cole-trapnell-lab.github.io/cufflinks/ | 20436464 |
eXpress | Transcriptome | Sequences | 2012 | //bio.math.berkeley.edu/eXpress/index.html | 23160280 |
IsoEM | Genome | Annotations | 2011 | http://dna.engr.uconn.edu/?page_id=105 | 21504602 |
MMSEQ | Transcriptome | Sequences | 2011 | https://github.com/eturro/mmseq | 21310039 |
RSEM | Transcriptome | Sequences | 2009 | http://deweylab.biostat.wisc.edu/rsem/ | 20022975, 21816040 |
rSeq | Transcriptome | Sequences | 2009 | http://www-personal.umich.edu/~jianghui/rseq/ | 19244387 |
Sailfish | N/A | Sequences | 2014 | http://www.cs.cmu.edu/~ckingsf/software/sailfish/ | 24752080 |
Scripture | Genome | Annotations | 2010 | https://www.broadinstitute.org/software/scripture/ | 20436462 |
TIGAR2 | Transcriptome | Sequences | 2013 | https://github.com/nariai/tigar2 | 23821651, 25560536 |