List of sequence alignment software: Difference between revisions

Revision as of 09:37, 15 March 2021

Revision as of 16:03, 22 March 2021

Line 81:

|-

| ScalaBLAST

| Highly parallel Scalable BLAST || Both || Oehmen et al.<ref>{{cite journal|

|last1=Oehmen |first1=C.|last2= Nieplocha |first2=J. |title=ScalaBLAST: A scalable implementation of BLAST for high-performance data-intensive bioinformatics analysis|journal=IEEE Transactions on Parallel & Distributed Systems |volume=17 |issue=8 |pages=740–749 |date=August 2006|

|doi=10.1109/TPDS.2006.112|s2cid=11122366|url=https://zenodo.org/record/1232261 }}</ref>||2011

|-

| Sequilab

Line 850:

| {{yes}}

| {{yes}}

| {{free}}, [[GNU General Public License|GPL]]3

| {{Free software; under the terms of GNU GPL v3}}

|<ref name="Marco-SolaSammeth2012">{{cite journal|last1=Marco-Sola|first1=Santiago|last2=Sammeth|first2=Michael|last3=Guigó|first3=Roderic|last4=Ribeca|first4=Paolo|title=The GEM mapper: fast, accurate and versatile alignment by filtration|journal=Nature Methods|volume=9|issue=12|year=2012|pages=1185–1188|issn=1548-7091|doi=10.1038/nmeth.2221|pmid=23103880|s2cid=2004416}}</ref>

|2012

Line 1,183:

| {{free}}, [[BSD licenses| {{free}}, [[BSD licenses|BSD]]]] derivative

|

<ref name="RumbleLacrouteDalcaFiumeSidowBrudno2009">{{cite journal|last1=Rumble|first1=Stephen M.|last2=Lacroute|first2=Phil|last3=Dalca|first3=Adrian V.|last4=Fiume|first4=Marc|last5=Sidow|first5=Arend|last6=Brudno|first6=Michael|title=SHRiMP: Accurate Mapping of Short Color-space Reads|journal=PLOS Computational Biology|

|volume=5|issue=5|year=2009|pages=e1000386|pmid=19461883|pmc=2678294|doi=10.1371/journal.pcbi.1000386|bibcode=2009PLSCB...5E0386R}}</ref>

<ref name="DavidDzambaListerIlieBrudno2011">{{cite journal|last1=David|first1=Matei|last2=Dzamba|first2=Misko|last3=Lister|first3=Dan|last4= Ilie|first4=Lucian|last5=Brudno|first5=Michael|title=SHRiMP2: Sensitive yet Practical Short Read Mapping|journal=Bioinformatics|volume=27|issue=7|year=2011|pages=1011–1012|pmid=21278192|doi=10.1093/bioinformatics/btr046|doi-access=free}}</ref>

| 2009-2011

Line 1,195:

| {{No}}

|

|<ref name="MalhisButterfieldEsterJones2009">{{cite journal|last1=Malhis|first1=Nawar|last2=Butterfield|first2=Yaron S. N.|last3=Ester|first3=Martin|last4=Jones|first4=Steven J. M.|title=Slider – Maximum use of probability information for alignment of short sequence reads and SNP detection|journal=Bioinformatics|

|volume=25|issue=1|year=2009|pages=6–13|pmid=18974170|pmc=2638935|doi=10.1093/bioinformatics/btn565}}</ref><ref name="MalhisJones2010">{{cite journal|last1=Malhis|first1=Nawar|last2=Jones|first2=Steven J. M.|title=High Quality SNP Calling Using Illumina Data at Shallow Coverage|journal=Bioinformatics|

|volume=26|issue=8|year=2010|pages=1029–1035|pmid=20190250|doi=10.1093/bioinformatics/btq092|doi-access=free}}</ref>

| 2009-2010

|-

Line 1,325:

==References==

{{Reflist|2}}

{{DEFAULTSORT:List Of Sequence Alignment Software}}