Search details
1.
Multi-CSAR: a web server for scaffolding contigs using multiple reference genomes.
Nucleic Acids Res
; 50(W1): W500-W509, 2022 07 05.
Article
in English
| MEDLINE | ID: mdl-35524553
2.
Clover: a clustering-oriented de novo assembler for Illumina sequences.
BMC Bioinformatics
; 21(1): 528, 2020 Nov 17.
Article
in English
| MEDLINE | ID: mdl-33203354
3.
CSAR-web: a web server of contig scaffolding using algebraic rearrangements.
Nucleic Acids Res
; 46(W1): W55-W59, 2018 07 02.
Article
in English
| MEDLINE | ID: mdl-29733393
4.
CSAR: a contig scaffolding tool using algebraic rearrangements.
Bioinformatics
; 34(1): 109-111, 2018 01 01.
Article
in English
| MEDLINE | ID: mdl-28968788
5.
iPARTS2: an improved tool for pairwise alignment of RNA tertiary structures, version 2.
Nucleic Acids Res
; 44(W1): W328-32, 2016 07 08.
Article
in English
| MEDLINE | ID: mdl-27185896
6.
R3D-BLAST2: an improved search tool for similar RNA 3D substructures.
BMC Bioinformatics
; 18(Suppl 16): 574, 2017 12 28.
Article
in English
| MEDLINE | ID: mdl-29297283
7.
Multi-CAR: a tool of contig scaffolding using multiple references.
BMC Bioinformatics
; 17(Suppl 17): 469, 2016 Dec 23.
Article
in English
| MEDLINE | ID: mdl-28155633
8.
CAR: contig assembly of prokaryotic draft genomes using rearrangements.
BMC Bioinformatics
; 15: 381, 2014 Nov 28.
Article
in English
| MEDLINE | ID: mdl-25431302
9.
Assembling contigs in draft genomes using reversals and block-interchanges.
BMC Bioinformatics
; 14 Suppl 5: S9, 2013.
Article
in English
| MEDLINE | ID: mdl-23734866
10.
R3D-BLAST: a search tool for similar RNA 3D substructures.
Nucleic Acids Res
; 39(Web Server issue): W45-9, 2011 Jul.
Article
in English
| MEDLINE | ID: mdl-21624889
11.
iPARTS: an improved tool of pairwise alignment of RNA tertiary structures.
Nucleic Acids Res
; 38(Web Server issue): W340-7, 2010 Jul.
Article
in English
| MEDLINE | ID: mdl-20507908
12.
SoRT2: a tool for sorting genomes and reconstructing phylogenetic trees by reversals, generalized transpositions and translocations.
Nucleic Acids Res
; 38(Web Server issue): W221-7, 2010 Jul.
Article
in English
| MEDLINE | ID: mdl-20538651
13.
An Integer Linear Programming Approach for Scaffolding Based on Exemplar Breakpoint Distance.
J Comput Biol
; 29(9): 961-973, 2022 09.
Article
in English
| MEDLINE | ID: mdl-35638936
14.
Sorting permutations by cut-circularize-linearize-and-paste operations.
BMC Genomics
; 12 Suppl 3: S26, 2011 Nov 30.
Article
in English
| MEDLINE | ID: mdl-22369173
15.
FASTR3D: a fast and accurate search tool for similar RNA 3D structures.
Nucleic Acids Res
; 37(Web Server issue): W287-95, 2009 Jul.
Article
in English
| MEDLINE | ID: mdl-19435878
16.
Reconstructing genome trees of prokaryotes using overlapping genes.
BMC Bioinformatics
; 11: 102, 2010 Feb 24.
Article
in English
| MEDLINE | ID: mdl-20181237
17.
SARSA: a web tool for structural alignment of RNA using a structural alphabet.
Nucleic Acids Res
; 36(Web Server issue): W19-24, 2008 Jul 01.
Article
in English
| MEDLINE | ID: mdl-18502774
18.
OGtree: a tool for creating genome trees of prokaryotes based on overlapping genes.
Nucleic Acids Res
; 36(Web Server issue): W475-80, 2008 Jul 01.
Article
in English
| MEDLINE | ID: mdl-18456706
19.
RE-MuSiC: a tool for multiple sequence alignment with regular expression constraints.
Nucleic Acids Res
; 35(Web Server issue): W639-44, 2007 Jul.
Article
in English
| MEDLINE | ID: mdl-17488842
20.
SPRING: a tool for the analysis of genome rearrangement using reversals and block-interchanges.
Nucleic Acids Res
; 34(Web Server issue): W696-9, 2006 Jul 01.
Article
in English
| MEDLINE | ID: mdl-16845100