Software-old: Difference between revisions

Revision as of 13:58, 9 July 2019

Below is a partial list of software packages installed on Sapelo2, Teaching (we are in the process of adding wiki pages for more applications). To view a list of all modules installed on Sapelo2/Teaching, along with a short description, please run the following command on Sapelo2/Teaching:

module spider

You can also use the command above to search for a specific application. For more information, please see Lmod.

Installed Software List

Last updated 2019-07-09. Note: Click on the icons to the right of the column headings to sort the table. 0-9 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

Name	Version	Category	Cluster
3D-DNA	180922	Bioinformatics	Sapelo2
4p	1.0	Bioinformatics	Sapelo2
ABySS	1.9.0, 2.0.2, 2.1.0	Bioinformatics	Sapelo2
ADMIXTURE	1.3.0	Bioinformatics	Sapelo2
aeneas	1.7.3	Other	Sapelo2
AFNI	17.3.05	Other	Sapelo2
ANGEL	2.5	Bioinformatics	Sapelo2
AIM-HII	0.5.5	Bioinformatics	Sapelo2
Albacore	2.3.4-cp35	Bioinformatics	Sapelo2
AlignGraph	20180709	Bioinformatics	Sapelo2
AlleleSeq_pipeline	1.2a	Bioinformatics	Sapelo2
ALLHiC	0.8.11	Bioinformatics	Sapelo2
Allim	1.2	Bioinformatics	Sapelo2
ALLMAPS	20190208	Bioinformatics	Sapelo2
AMBER	14, 16, 18	Chemistry	Sapelo2
AMBER	14	Chemistry	Teaching
AMOS	3.1.0	Bioinformatics	Sapelo2
Anaconda2	5.0.1, 2018.12, 2019.03	Programming	Sapelo2
Anaconda3	5.0.1, 2018.12, 2019.03	Programming	Sapelo2
annovar	2017Jul16	Bioinformatics	sapelo2
ANSYS	18.2, 19.2	Engineering	Sapelo2
anvi'o	4, 5.1, 5.3, 5.4	Bioinformatics	sapelo2
Aragorn	1.2.38	Bioinformatics	Sapelo2
Arlequin	3.5.2.2	Bioinformatics	Sapelo2
ART	20160605	Bioinformatics	Sapelo2
ARCS	1.0.5	Bioinformatics	Sapelo2
Artemis	17.0.1	Bioinformatics	Sapelo2
Artemis	17.0.1	Bioinformatics	Teaching
ASTRAL	5.6.1	Bioinformatics	Sapelo2
ATk	2.22.0	Other	Sapelo2
ATLAS	3.10.2	Other	Sapelo2
AUGUSTUS	3.2.3, 3.3.2	Bioinformatics	Sapelo2
AUGUSTUS	3.2.3	Bioinformatics	Teaching
BamTools	2.4.1	Bioinformatics	Sapelo2
Barrnap	0.9	Bioinformatics	Sapelo2
basespace-cli	0.9.17	Bioinformatics	Sapelo2
BayesAss	3.0.4	Bioinformatics	Sapelo2
Bazel	0.8.1, 0.11.1	Other	Sapelo2
BBMap	37.67	Bioinformatics	Sapelo2
BCFtools	1.1, 1.3.1, 1.6, 1.8, 1.9	Bioinformatics	Sapelo2
BCFtools	1.3.1, 1.6, 1.8	Bioinformatics	Teaching
bcl2fastq	2.20.0	Bioinformatics	Sapelo2
Beast	1.8.4, 1.10.1, 1.10.3, 1.10.4, 2.4.8pre, 2.4.8, 2.5.0, 2.5.1	Bioinformatics	Sapelo2
BEDOPS	2.4.30	Bioinformatics	Sapelo2
BEDTools	2.17.0, 2.26.0, 2.28.0	Bioinformatics	Sapelo2
BEDTools	2.26.0	Bioinformatics	Teaching
bioawk	1.0	Bioinformatics	Sapelo2
BioKanga	21.0.0	Bioinformatics	Sapelo2
Biom-format	2.1.7	Bioinformatics	Sapelo2
BionanoSolve	3.2.1-04122018, 3.2.2-08222018 3.3-10252018	Bioinformatics	Sapelo2
BioPerl	1.7.1	Bioinformatics	Sapelo2
BioPerl	1.7.1	Bioinformatics	Teaching
BioPython	1.68	Bioinformatics	Sapelo2
Biopython	1.68	Bioinformatics	Teaching
Bismark	0.20.0	Bioinformatics	Sapelo2
Bison	2.7, 3.0.2, 3.0.4	Other	Sapelo2
BLASR	2.2	Bioinformatics	Sapelo2
BLAST+	2.2.31, 2.6.0, 2.7.1, 2.9.0	Bioinformatics	Sapelo2
BLAST+	2.6.0	Bioinformatics	Teaching
BLAST	2.2.26	Bioinformatics	Sapelo2
BLAST	2.2.26	Bioinformatics	Teaching
BLAT	3.4, 3.5	Bioinformatics	Sapelo2
Blosc	1.12.1	Library	Sapelo2
Boost	1.54.0, 1.61.0, 1.63.0, 1.65.1	Library	Sapelo2
Boto3	1.9.14	Other	Sapelo2
bowtie2	2.2.3, 2.3.3, 2.3.4.1	Bioinformatics	Sapelo2
Bowtie2	2.2.3, 2.3.3, 2.3.4.1	Bioinformatics	Teaching
Bowtie	1.2.2	Bioinformatics	Sapelo2
Bracken	2.2	Bioinformatics	Sapelo2
braker	2.0.5	Bioinformatics	Sapelo2
BreakDancer	1.4.5-foss-2016b	Bioinformatics	Sapelo2
BS-Seeker2	2.1.5	Bioinformatics	Sapelo2
BUSCO	2.0, 3.0.2	Bioinformatics	Sapelo2
BUSCO	3.0.2	Bioinformatics	Teaching
BWA	0.7.15, 0.7.17	Bioinformatics	Sapelo2
BWA	0.7.17, 0.7.15	Bioinformatics	Teaching
Caffe	04082018	Other	Sapelo2
cactus	1.0	Bioinformatics	Sapelo2
cairo	1.14.6, 1.14.10, 1.14.12	Bioinformatics	Sapelo2
Canu	1.7, 1.7.1	Bioinformatics	Sapelo2
Canu	1.4, 1.5, 1.6, 1.7	Bioinformatics	Teaching
CAP-miRSeq	05/20184	Bioinformatics	Sapelo2
CAP3	03092015	Bioinformatics	Sapelo2
CD-HIT	4.6.1-2012-08-27, 4.6.8	Bioinformatics	Sapelo2
CDNA_Cupcake	5.9, 7.2	Bioinformatics	Sapelo2
CellProfiler	3.1.8	Bioinformatics	Sapelo2
Cellrange	3.0.1	Bioinformatics	Sapelo2
CENSOR	4.2.29	Bioinformatics	Sapelo2
CFITSIO	3.38	Library	Sapelo2
CFOUR	1.2, 2.00-beta	Chemistry	Sapelo2
CGAL	4.11	Library	Sapelo2
Cgmaptools	0.1.1	Bioinformatics	Sapelo2
Cgview_comparison_tool	2017.09.19	Bioinformatics	Sapelo2
CheckM	1.0.12	Bioinformatics	Sapelo2
Chimera	1.13	Bioinformatics	Sapelo2
Chimera	1.13	Bioinformatics	Teaching
Chromosomer	0.1.3, 0.1.4a0	Bioinformatics	Sapelo2
Chromosomer	0.1.4a	Bioinformatics	Teaching
circlator	1.5.3	Bioinformatics	Sapelo2
Circos	0.69-6	Bioinformatics	Sapelo2
Cleaveland4	4.4	Bioinformatics	Sapelo2
Click	7.0	Other	Sapelo2
Clust	1.9.0	Bioinformatics	Sapelo2
Clustal-Omega	1.2.4	Bioinformatics	Sapelo2
ClustalW2	2.1	Bioinformatics	Sapelo2
CMake	3.0.0, 3.4.3, 3.5.2, 3.6.1, 3.6.2, 3.7.2, 3.8.0, 3.9.1, 3.9.5, 3.10.2	Other	Sapelo2
CNVnator	0.3.3	Bioinformatics	Sapelo2
Cogent	3.5	Bioinformatics	Sapelo2
Consed	29.0	Bioinformatics	Sapelo2
cooler	0.8.5	Bioinformatics	Sapelo2
CPLEX	12.6.3	Engineering	Sapelo2
crest	1.0	Bioinformatics	Sapelo2
CRISPResso	1.0.13	Bioinformatics	Sapelo2
CUDA	7.0.28, 7.5.18, 8.0.61, 8.0.61_375.26-GCC-5.4.0-2.26, 9.0.176, 9.1.85, 9.2.88	Programming	Sapelo2
cuDNN	7.0.4, 7.2.1.38, 7.4.2.24	Programming	Sapelo2
Cufflinks	2.2.1	Bioinformatics	Sapelo2
Cufflinks	2.2.1	Bioinformatics	Teaching
cURL	7.49.1	Other	Sapelo2
cutadapt	1.9.1, 1.14, 1.16	Bioinformatics	Sapelo2
Cython	0.27.3, 0.28.5	Programming	Sapelo2
CythonGSL	0.2.2	Other	Sapelo2
Danpos2	2.2.2	Bioinformatics	Sapelo2
Darknet	3	Other	Sapelo2
DBG2OLC	20170208	Bioinformatics	Sapelo2
DBG2OLC	20170208	Bioinformatics	Teaching
DDocent	2.7.8	Bioinformatics	Sapelo2
DDSCAT	7.3.2	Chemistry	Sapelo2
deepTools	3.0.2, 3.2.1	Bioinformatics	Sapelo2
DeepVariant	0.7.0	Bioinformatics	Sapelo2
Delft3d	20190610	Other	Sapelo2
DendroPy	4.3.0	Bioinformatics	Sapelo2
detectMITE	20170425	Bioinformatics	Sapelo2
detonate	1.11	Bioinformatics	Sapelo2
DIAMOND	0.8.31, 0.9.19, 0.9.22, 0.9.24	Bioinformatics	Sapelo2
DIAMOND	1.0	Bioinformatics	Teaching
DISCOVARdenovo	52488	Bioinformatics	Sapelo2
DiscoVista	20190429	Bioinformatics	Sapelo2
Distruct	2.2	Bioinformatics	Sapelo2
DLCpar	1.0	Bioinformatics	Sapelo2
Doxygen	1.8.7, 1.8.11, 1.8.13	Other	Sapelo2
dRep	2.3.0	Bioinformatics	Sapelo2
DSSP	3.0.7	Bioinformatics	Sapelo2
DyNet	2.1	Other	Sapelo2
EDGE-pro	1.3.1	Bioinformatics	Sapelo2
EggNOG-Mapper	1.0.3	Bioinformatics	Sapelo2
Eigen	3.2.3, 3.3.5	Library	Sapelo2
EIGENSOFT	6.1.4, 7.2.1	Bioinformatics	Sapelo2
EIGENSOFT	6.1.4, 7.2.1	Bioinformatics	Teaching
EMBOSS	6.6.0	Bioinformatics	Sapelo2
EMBOSS	6.6.0	Bioinformatics	Teaching
EMMAX beta	beta	Bioinformatics	Sapelo2
Ensembl-VEP	20180914	Bioinformatics	Sapelo2
EnTAP	0.8.4 beta	Bioinformatics	Sapelo2
epic2	0.0.36	Bioinformatics	Sapelo2
EricScript	0.5.5	Bioinformatics	Sapelo2
ESMF	7.0.2	Other	Sapelo2
eSpeak	1.48.04	Other	Sapelo2
Ete	3.1.1	Bioinformatics	Sapelo2
EVcouplings	0.0.5	Bioinformatics	Sapelo2
EVidenceModeler	0.1.3	Bioinformatics	Sapelo2
Exonerate	2.4.0	Bioinformatics	Sapelo2
Exonerate	2.4.0	Bioinformatics	Teaching
FALCON	02282018_unzip	Bioinformatics	Sapelo2
Fast-Plast	1.2.6	Bioinformatics	Sapelo2
FASTA	36.3.5e	Bioinformatics	Sapelo2
FastME	2.1.5	Bioinformatics	Sapelo2
FastQC	0.11.5,0.11.8	Bioinformatics	Sapelo2
FastQValidator	0.1.1a	Bioinformatics	Sapelo2
FastSTRUCTURE	1.0	Bioinformatics	Sapelo2
FastTree	2.1.10	Bioinformatics	Sapelo2
FastViromeExplorer	20180918	Bioinformatics	Sapelo2
FASTX-Toolkit	0.0.14	Bioinformatics	Sapelo2
FFmpeg	3.1.3, 3.4.1	Other	Sapelo2
FFTW	3.3.4, 3.3.6, 3.3.7	Math Library	Sapelo2
FIAT	1.6.0	Other	Sapelo2
fineSTRUCTURE	2.1.3	Bioinformatics	Sapelo2
FLASH	1.2.11	Bioinformatics	Sapelo2
FLTK	1.3.4	Other	Sapelo2
Flye	2.3.6	Bioinformatics	Sapelo2
FoX	4.1.2	Library	Sapelo2
Freebayes	1.2.0	Bioinformatics	Sapelo2
Freebayes	1.2.0	Bioinformatics	Teaching
FriBidi	1.0.1	Library	Sapelo2
Funannotate	1.5.0	Bioinformatics	Sapelo2
FuzzyWuzzy	0.17.0	Other	Sapelo2
fxtract	2.3	Bioinformatics	Sapelo2
GAG	2.0.1	Bioinformatics	Sapelo2
GAG	2.0.1	Bioinformatics	Teaching
GAMESS	14Feb2018	Chemistry	Sapelo2
GapFiller	2.1.1	Bioinformatics	Sapelo2
GapFiller	2.1.1	Bioinformatics	Teaching
GAPIT	20180524	Bioinformatics	Sapelo2
GAPPadder	0.1	Bioinformatics	Sapelo2
GARLI	2.01	Bioinformatics	Sapelo2
GATK	3.4-0, 3.8-0, 3.8-1, 4.0.3.0, 4.0.11.0, 4.1.0.0	Bioinformatics	Sapelo2
GATK	3.8-0, 3.4-0	Bioinformatics	Teaching
GAUSSIAN	09	Chemistry	Sapelo2
GAUSSIAN	09	Chemistry	Teaching
GaussView	5	Chemistry	Sapelo2
GaussView	5	Chemistry	Teaching
GBlocks	0.91b	Bioinformatics	Sapelo2
GCTA	1.26.0	Bioinformatics	Sapelo2
GD	2.66	Bioinformatics	Sapelo2
GDAL	2.1.0, 2.2.2	Library	Sapelo2
gdc-client	1.3.0	Bioinformatics	Sapelo2
Gdk-pixbuf	2.36.0	Library	Sapelo2
GEAN	0.1	Bioinformatics	Sapelo2
GEM-library	20130406-045632	Bioinformatics	Sapelo2
GeneMark.hmm.eukaryotic	4.30	Bioinformatics	Sapelo2
GeneMarkES	4.33	Bioinformatics	Sapelo2
GeneMarkES	4.33	Bioinformatics	Teaching
GeneMarkS-T	4.33	Bioinformatics	Sapelo2
GeneMarkS	4.30	Bioinformatics	Sapelo2
GenericRepeatFinder	1.0	Bioinformatics	Sapelo2
Genome	Phred version: 0.071220.c, Phrap version: 0.990329, Consed version: 29.0	Bioinformatics	Sapelo2
GenomeTools	1.5.9	Bioinformatics	Sapelo2
Genrich	0.5	Bioinformatics	Sapelo2
GEOS	3.6.2	Library	Sapelo2
GET_HOMOLOGUES	1.7.6	Bioinformatics	Teaching
Gffcompare	0.10.4	Bioinformatics	Sapelo2
gffread	0.9.12	Bioinformatics	Sapelo2
GFlow	0.1.7	Library	Sapelo2
Ghostscript	9.20, 9.22	Other	Sapelo2
GISTIC	2.0.3	Bioinformatics	Sapelo2
Gkin	1.1	Bioinformatics	Sapelo2
GL2PS	1.4.0	Library	Sapelo2
GLib	2.49.5, 2.53.5, 2.54.3	Library	Sapelo2
GLIMMER	3.02b	Bioinformatics	Sapelo2
GLIMMER	3.02b	Bioinformatics	Teaching
GLPK	4.63, 4.65	Programming	Sapelo2
GMAP-GSNAP	2016-11-07, 2018-07-04	Bioinformatics	Sapelo2
GMP	4.3.2, 6.1.1, 6.1.2	Library	Sapelo2
gnuplot	5.0.5	Graphics	Sapelo2
GObject-Introspection	1.49.1, 1.54.1	Other	Sapelo2
grace	5.1.25	Graphics	Sapelo2
GraftM	0.11.1	Bioinformatics	Sapelo2
GraphicsMagicK	1.3.28	Other	Sapelo2
Graphviz	2.40.1	Other	Sapelo2
GROCSVs	0.2.5	Bioinformatics	Sapelo2
Gromacs	2016.4, 2018.1	Chemistry	Sapelo2
GSL	1.16, 2.1, 2.3. 2.4	Math Library	Sapelo2
GStreamer	1.14.0	Bioinformatics	Sapelo2
GTDBTk	0.2.2	Bioinformatics	Sapelo2
GTK+	2.24.31	Library	Sapelo2
GTS	0.7.6	Library	Sapelo2
Guile	1.8.8	Other	Sapelo2
h5py	2.7.1	Other	Sapelo2
HapCUT2	20190606	Bioinformatics	Sapelo2
HarfBuzz	1.3.1, 1.7.5	Other	Sapelo2
HARP	140925_103521	Bioinformatics	Sapelo2
Harvest	1.1.2	Bioinformatics	Teaching
HarvestTools	1.2	Bioinformatics	Sapelo2
HH-suite	3.0-beta.3	Bioinformatics	Sapelo2
HiC-Pro	2.11.0-beta	Bioinformatics	Sapelo2
hindex	1.42	Bioinformatics	Sapelo2
HISAT2	2.1.0	Bioinformatics	Sapelo2
HISAT2	2.1.0	Bioinformatics	Teaching
HMMER	2.3, 3.1b2	Bioinformatics	Sapelo2
Homer	4.9.1, 4.10	Bioinformatics	Sapelo2
HPCGridRunner	1.0.2	Tools	Sapelo2
htop	2.0.1	Other	Sapelo2
HTSeq	0.9.1	Bioinformatics	Sapelo2
HTSeq	0.9.1	Bioinformatics	Teaching
HTSlib	1.3.2, 1.6, 1.8	Library	Sapelo2
HUMAnN2	0.11.2	Bioinformatics	Sapelo2
HybPiper	1.3.1	Bioinformatics	Sapelo2
Hypre	2.11.1	Library	Sapelo2
ICORN2	0.95	Bioinformatics	Sapelo2
IDBA-UD	1.1.3	Bioinformatics	Sapelo2
IGV	2.4.4	Bioinformatics	Sapelo2
IGV	2.4.4	Bioinformatics	Teaching
IGVTools	2.3.98	Bioinformatics	Sapelo2
ImageMagick	7.0.5, 7.0.7	Other	Sapelo2
Infernal	1.1.2	Bioinformatics	Sapelo2
IonCom	20190521	Bioinformatics	Sapelo2
iprscan (InterProScan)	5.29-68.0, 5.31-70.0, 5.32-71.0	Bioinformatics	Sapelo2
ipyrad	0.7.24, 0.7.28, 0.7.30	Bioinformatics	Sapelo2
Ipyrad	0.7.24	Bioinformatics	Teaching
IPython	5.3.0, 6.2.1, 7.5.0	Other	Sapelo2
IQ-Tree	1.5.5, 1.6.5	Bioinformatics	Sapelo2
IRMA	0.6.7	Bioinformatics	Sapelo2
IsONclust	0.0.4	Bioinformatics	Sapelo2
IsoSeq3	3.1.2	Bioinformatics	Sapelo2
ITSTool	2.0.4	Utility	Sapelo2
JAGS	4.3.0	Statistics	Sapelo2
JasPer	1.900.1, 2.0.12	Other	Sapelo2
Java	1.8.0_92, 1.8.0_112, 1.8.0_121, 1.8.0_141, 1.8.0_144, 1.8.0_202	Programming	Sapelo2
Java	1.8.0_92, 1.8.0_112, 1.8.0_121, 1.8.0_141, 1.8.0_144	Programming	Teaching
jcvi	0.8.12	Bioinformatics	Sapelo2
Jellyfish	2.2.6	Bioinformatics	Sapelo2
JModelTest	2.1.10	Bioinformatics	Sapelo2
Juicer	1.5.6	Bioinformatics	Sapelo2
JUnit	4.12	Other	Sapelo2
Jupyter	4.3.0	Other	Sapelo2
Kaiju	1.6.2	Bioinformatics	Sapelo2
kallisto	0.43.1	Bioinformatics	Sapelo2
KAT	2.4.1	Bioinformatics	Sapelo2
keras	2.0.6, 2.2.2	Other	Sapelo2
KinFin	1.0.3	Bioinformatics	Sapelo2
KmerGenie	1.7044	Bioinformatics	Sapelo2
KmerGenie	1.7044	Bioinformatics	Teaching
Kraken2	2.0.7-beta	Bioinformatics	Sapelo2
KronaTools	2.7	Bioinformatics	Sapelo2
LAME	3.100	Other	Sapelo2
LAMMPS	30Jul16, 11Aug17	Chemistry	Sapelo2
LAPACK	3.6.1	Other	Sapelo2
LAST	956, 959	Bioinformatics	Sapelo2
LASTZ	1.04.00	Bioinformatics	Sapelo2
LDhat	2.2	Bioinformatics	Sapelo2
LDhelmet	1.10	Bioinformatics	Sapelo2
Lep-MAP3	0.2	Bioinformatics	Sapelo2
LibStatGen	1.0.14	Bioinformatics	Sapelo2
LibTIFF	4.0.6, 4.0.8, 4.0.9	Library	Sapelo2
LINKS	1.8.7	Bioinformatics	Sapelo2
LittleCMS	2.8	Other	Sapelo2
LLVM	3.8.1, 4.0.0, 5.0.1, 6.0.0	Library	Sapelo2
LMDB	0.9.22	Bioinformatics	Sapelo2
LoFreq	2.1.2	Bioinformatics	Sapelo2
Log-Log4perl	1.49	Other	Sapelo2
LongRanger	2.2.2	Bioinformatics	Sapelo2
LoRDEC	0.9	Bioinformatics	Sapelo2
LRCstats	1.1	Bioinformatics	Sapelo2
lrslib	6.2	Other	Sapelo2
LS-DYNA	10.123355	Engineering	Sapelo2
LS-PrePost	4.5	Engineering	Sapelo2
LtrDetector	1.0	Bioinformatics	Sapelo2
LTR_Finder	1.0.7	Bioinformatics	Sapelo2
LTR_retriever	1.6	Bioinformatics	Sapelo2
LUMPY	0.2.13	Bioinformatics	Sapelo2
LZO	2.10	Bioinformatics	Sapelo2
M4	1.4.16, 1.4.17, 1.4.17	Other	Sapelo2
MACS2	2.1.1, 2.1.2	Bioinformatics	Sapelo2
MAFFT	7.273, 7.313, 7.397, 7.407	Bioinformatics	Sapelo2
MAFFT	7.130, 7.273, 7.313	Bioinformatics	Teaching
Magic-BLAST	1.4.0	Bioinformatics	Sapelo2
Magma-GPU	2.3.0	Other	Sapelo2
Magma	2.22-9, 2.24-4	Other	Sapelo2
mahotas	1.4.3	Bioinformatics	Sapelo2
Maker	3.01.02-beta,2.31.9, 2.31.10	Bioinformatics	Sapelo2
Maker	2.31.9	Bioinformatics	Teaching
Mako	1.0.4, 1.0.7	Other	Sapelo2
MARVEL	20180918	Bioinformatics	Sapelo2
Mash	2.1	Bioinformatics	Sapelo2
MaSuRCA	3.2.2, 3.2.9, 3.3.1	Bioinformatics	Sapelo2
Matlab	R2017b, R2018b	Programming	Sapelo2
Matlab	R2018b	Programming	Teaching
Matplotlib	1.5.3, 2.0.2, 2.1.0, 2.1.2, 2.2.3, 3.0.0	Other	Sapelo2
Mauve	2015-02-13	Bioinformatics	Sapelo2
Maven	3.5.2	Bioinformatics	Sapelo2
Mawk	1.3.4	Other	Sapelo2
MCL	14.137	Bioinformatics	Sapelo2
MCScanX	0.8	Bioinformatics	Sapelo2
MEGA	7.0.26-1	Bioinformatics	Sapelo2
MEGAHIT	1.1.1, 1.1.3	Bioinformatics	Sapelo2
MeGAMerge	3.0.1	Bioinformatics	Sapelo2
MEME	4.11.0, 5.0.0_1	Bioinformatics	Sapelo2
Meraculous	2.2.5	Bioinformatics	Sapelo2
Mercurial	4.4.2	Other	Sapelo2
Mesa	12.0.2, 17.3.6	Other	Sapelo2
MET	7.0	Other	Sapelo2
MetaBAT	2.12.1	Bioinformatics	Sapelo2
MetaCLADE	1.1	Bioinformatics	Sapelo2
MetaPhlAn	1.7.7	Bioinformatics	Sapelo2
MetaPhlAn2	2.7.8	Bioinformatics	Sapelo2
methylpy	1.2.9, 1.3.2	Bioinformatics	Sapelo2
METIS	5.1.0	Other	Sapelo2
MG-RAST-Tools	1.1	Bioinformatics	Sapelo2
minced	0.2.1	Bioinformatics	Sapelo2
Minia	3.2.0	Bioinformatics	Sapelo2
miniasm	0.3	Bioinformatics	Sapelo2
Miniconda3	4.4.10	Other	Sapelo2
minimap2	2.10, 2.13	Bioinformatics	Sapelo2
MIonSite	20190528	Bioinformatics	Sapelo2
mirdeep-p	1.3	Bioinformatics	Sapelo2
miRDeep2	0.0.8	Bioinformatics	Sapelo2
MiRDP2	1.1.2	Bioinformatics	Sapelo2
MITE-Hunter	11-2011	Bioinformatics	Sapelo2
MITE-Tracker	0.1	Bioinformatics	Sapelo2
MOTECC_qmdcp	90	Chemistry	Teaching
Mothur	1.39.5	Bioinformatics	Sapelo2
motif	2.3.5, 2.3.8	Graphics	Sapelo2
MPJ-Express	0.44	Library	Sapelo2
MrBayes	3.2.6	Bioinformatics	Sapelo2
MREPS	1.0.5	Bioinformatics	Sapelo2
ms	20140304	Bioinformatics	Teaching
MSTmap	20181130	Bioinformatics	Sapelo2
MultiQC	1.5	Bioinformatics	Sapelo2
MUMmer	3.23, 4.0.0beta2	Bioinformatics	Sapelo2
MUMmer	3.23	Bioinformatics	Teaching
MUSCLE	3.8.1551, 3.8.31	Bioinformatics	Sapelo2
MuTect	1.1.7	Bioinformatics	Sapelo2
muver	0.1.0	Bioinformatics	Sapelo2
mvqtlcim	1.0	Bioinformatics	Sapelo2
MZmine2	2.40.1	Bioinformatics	Sapelo2
NAMD	2.12	Chemistry	Sapelo2
Nanocorr	5.9	Bioinformatics	Sapelo2
Nanopolish	0.10.2	Bioinformatics	Sapelo2
NASM	2.11, 2.12, 2.13	Other	Sapelo2
NCCL	2.4.2	Other	Sapelo2
NCL	6.4.0, 6.5.0	Other	Sapelo2
NCL	6.4.0, 6.5.0	Other	Teaching
ncview	2.1.7	Graphics	Sapelo2
NCO	4.7.4	Other	Sapelo2
NCO	4.7.4	Other	Teaching
Necklace	1.01	Bioinformatics	Sapelo2
NeEstimator	2.1	Bioinformatics	Sapelo2
Newbler	3.0	Bioinformatics	Sapelo2
Nextflow	18.10.1	Bioinformatics	Sapelo2
NextGenMap	0.5.5	Bioinformatics	Sapelo2
ngmlr	0.2.6-beta	Bioinformatics	Sapelo2
NGmerge	0.3	Bioinformatics	Sapelo2
NGS	1.3.0	Bioinformatics	Sapelo2
NGSQCToolkit	2.3.3	Bioinformatics	Sapelo2
nhPhyML	20180515	Bioinformatics	Sapelo2
NiBabel	2.2.1	Other	Sapelo2
nistats	0.0.1a0	Other	Sapelo2
NLopt	2.4.2	Library	Sapelo2
Nseg	20180530	Bioinformatics	Sapelo2
NucleoATAC	0.3.4	Bioinformatics	Sapelo2
NWChem	6.8	Chemistry	Sapelo2
Oases	0.2.08, 0.2.09	Bioinformatics	Sapelo2
OCaml	4.01.0, 4.02.3	Programming	Sapelo2
OpenBUGS	3.2.3	Statistics	Sapelo2
OpenCV	3.4.1	Other	Sapelo2
OpenJPEG	2.3.0	Other	Sapelo2
OpenSlide	3.4.1	Other	Sapelo2
OpenSlide-Python	1.1.1	Other	Sapelo2
ORCA	3.0.3, 4.0.0.2, 4.0.1.2, 4.1.0, 4.1.1	Chemistry	Sapelo2
OrfM	0.6.1	Bioinformatics	Sapelo2
OrganelleRef_PBA	1.0.8	Bioinformatics	Sapelo2
ORGanelle_ASeMbler	0.2.03	Bioinformatics	Sapelo2
ORGASM	0.2.03	Bioinformatics	Sapelo2
ORP	2.0.0, 2.2.2	Bioinformatics	Sapelo2
OrthoFinder	2.1.2, 2.2.7	Bioinformatics	Sapelo2
OrthoFinder	2.1.2	Bioinformatics	Teaching
OrthoMCL	2.0.9	Bioinformatics	Sapelo2
p7zip	16.02	Other	Sapelo2
PAGIT	1.64	Bioinformatics	Sapelo2
Pairix	0.3.7	Bioinformatics	Sapelo2
pairtools	0.3.0	Bioinformatics	Sapelo2
Pal_finder	0.02.04	Bioinformatics	Sapelo2
PAML	4.9h	Bioinformatics	Sapelo2
PAML	4.9h	Bioinformatics	Teaching
PANDAseq	2.5	Bioinformatics	Sapelo2
Pango	1.40.3, 1.41.1	Library	Sapelo2
Parliament2	0.1.8, hgsc	Bioinformatics	Sapelo2
Parsnp	1.2	Bioinformatics	Sapelo2
PartitionFinder	2.1.1	Bioinformatics	Sapelo2
PartitionFinder	2.1.1	Bioinformatics	Teaching
PASA	2.3.3	Bioinformatics	Sapelo2
PASTA	1.8.2	Bioinformatics	Sapelo2
PASTA	1.8.2	Bioinformatics	Teaching
PAUP	4a165_centos64	Bioinformatics	Sapelo2
Pb-assembly	0.0.2	Bioinformatics	Sapelo2
pbh5tools	0.8.0	Bioinformatics	Sapelo2
PBLAT	2.0.0	Bioinformatics	Sapelo2
pbmm2	1.0.0	Bioinformatics	Sapelo2
PBSuite	15.8.24	Bioinformatics	Sapelo2
PCRE	8.38, 8.39, 8.41	Library	Sapelo2
PeakRanger	1.18	Bioinformatics	Sapelo2
PEAR	0.9.8	Bioinformatics	Sapelo2
Perl	5.20.3, 5.24.0, 5.24.1, 5.26.0, 5.26.1	Programming	Sapelo2
Perl	5.26.1, 5.26.0, 5.24.1, 5.24.0, 5.20.3	Programming	Teaching
PETSc	3.8.4	Math Library	Sapelo2
PGDBG	18.10	Debugger	Sapelo2
PGDSpider	2.1.1.5	Bioinformatics	Sapelo2
PhaseGenomics	20181220	Bioinformatics	Sapelo2
phaser	1.2.0	Bioinformatics	Sapelo2
PhaseTank	1.0	Bioinformatics	Sapelo2
PHASIS	3.3	Bioinformatics	Sapelo2
Phobius	1.01	Bioinformatics	Sapelo2
Phred/Phrap/Conced	Phred version: 0.071220.c, Phrap version: 0.990329, Consed version: 29.0	Bioinformatics	Sapelo2
Phycas	2.2.0	Bioinformatics	Sapelo2
PHYLIP	3.697	Bioinformatics	Sapelo2
PhyloBayes-MPI	20161021	Bioinformatics	Sapelo2
PhyloCSF	20180919	Bioinformatics	Sapelo2
Phyluce	1.6.1	Bioinformatics	Sapelo2
PhyML	3.3.20170530	Bioinformatics	Sapelo2
PhyParts	0.0.1	Bioinformatics	Sapelo2
picard	2.16.0	Bioinformatics	Sapelo2
Picard	2.16.0	Bioinformatics	Teaching
PICRUSt	1.1.3	Bioinformatics	Sapelo2
pigz	2.3.3	Other	Sapelo2
PIL	1.1.7	Library	Sapelo2
PILER	2.5	Bioinformatics	Sapelo2
Pilon	1.22	Bioinformatics	Sapelo2
Pilon	1.22	Bioinformatics	Teaching
PLINK	1.07, 1.9b	Bioinformatics	Sapelo2
Plmc	0.1	Bioinformatics	Sapelo2
Porechop	0.2.4	Bioinformatics	Sapelo2
PoSSuMsearch	2.0	Bioinformatics	Sapelo2
Pplacer	1.1.alpha19	Bioinformatics	Sapelo2
Praat	6048-Linux64-nogui	Other	Sapelo2
PRANK	170427	Bioinformatics	Sapelo2
PRAPI	2.0	Bioinformatics	Sapelo2
Primer3	2.3.7	Bioinformatics	Sapelo2
PRINSEQ	0.20.4	Bioinformatics	Sapelo2
Prodigal	2.6.3	Bioinformatics	Sapelo2
progressiveCactus	0.1	Bioinformatics	Sapelo2
PROJ	4.9.2	Other	Sapelo2
Prokka	1.13	Bioinformatics	Sapelo2
Prokka	1.13	Bioinformatics	Teaching
proovread	2.14.1	Bioinformatics	Sapelo2
Proovread	2.14.1	Bioinformatics	Teaching
protobuf	3.3.0, 3.4.0, 3.6.0	Other	Sapelo2
psmc	0.6.5	Bioinformatics	Sapelo2
pybedtools	0.7.10	Bioinformatics	Sapelo2
pyDNA	0.1	Bioinformatics	Sapelo2
pydub	0.22.1	Other	Sapelo2
pyfasta	0.5.2	Bioinformatics	Sapelo2
PyMOL	2.3.0a0	Graphics	Sapelo2
pyNBS	0.2.0	Bioinformatics	Sapelo2
PyPy	6.0.0 (2.7.14)	Programming	Sapelo2
Pysam	0.10.0, 0.13.0, 0.14.1	Bioinformatics	Sapelo2
Python	2.7.12, 2.7.14, 3.5.2, 3.6.4, 3.7.0	Programming	Sapelo2
Python	3.6.4, 3.5.2, 2.7.14, 2.7.12	Programming	Teaching
PyTorch	0.3.1, 1.0.0	Other	Sapelo2
q2-brocc	2018.6.0.dev0	Bioinformatics	Sapelo2
qiaseq-16S	20190306	Bioinformatics	Sapelo2
QIIME2	2018.2, 2018.4, 2018.6, 2018.8, 2018.11, 2019.1	Bioinformatics	Sapelo2
QIIME2	2018.4, 2018.6, 2018.8	Bioinformatics	Teaching
QIIME	1.9.1	Bioinformatics	Sapelo2
QTLcartographer	1.17j	Bioinformatics	Sapelo2
Qualimap2	2.2.1	Bioinformatics	Sapelo2
Quantum Espresso	6.2.0, 6.3.0-QMCPACK-3.6.0-patch	Chemistry	Sapelo2
QUAST	4.2, 4.6.1, 4.6.3, 5.0.0, 5.0.2	Bioinformatics	Sapelo2
QMCPACK	3.6.0	Chemistry	Sapelo2
R	3.4.4	Statistics	Sapelo2
R	3.4.4	Statistics	Teaching
racon	20180406	Bioinformatics	Sapelo2
randfold	2.0.1	Bioinformatics	Sapelo2
RATT	20180710	Bioinformatics	Sapelo2
RAxML-NG	0.7.0	Bioinformatics	Sapelo2
RAxML	8.2.4, 8.2.11	Bioinformatics	Sapelo2
RAxML	8.2.11	Bioinformatics	Teaching
Ray	2.3.1	Bioinformatics	Sapelo2
Rcorrector	1.0.2	Bioinformatics	Sapelo2
Realphy	1.1.2	Bioinformatics	Sapelo2
REAPR	1.0.18	Bioinformatics	Sapelo2
RECON	1.08	Bioinformatics	Sapelo2
Redundans	0.14a	Bioinformatics	Sapelo2
RepeatExplorer-TAREAN	11/09/2018	Bioinformatics	Sapelo2
RepeatMasker	4.0.5, 4.0.7	Bioinformatics	Sapelo2
RepeatMasker	4.0.7	Bioinformatics	Teaching
Repeatmodeler	1.0.11	Bioinformatics	Sapelo2
RepeatModeler	1.0.11	Bioinformatics	Teaching
RepeatScout	1.05	Bioinformatics	Sapelo2
RepeatScout	1.05	Bioinformatics	Teaching
REPET	2.5	Bioinformatics	Sapelo2
RevBayes	1.0.10	Bioinformatics	Sapelo2
RevBayes	1.0.10	Bioinformatics	Teaching
rjags	4.6	Other	Sapelo2
RMBlast	2.6.0	Bioinformatics	Sapelo2
Rmpi	0.6-6	Programming	Sapelo2
RNAmmer	1.2	Bioinformatics	Sapelo2
RNAz	2.1	Bioinformatics	Sapelo2
Roary	3.12.0	Bioinformatics	Sapelo2
Rosetta	2017.45.59812	Chemistry	Sapelo2
RSEM	1.3.0, 1.3.1	Bioinformatics	Sapelo2
Rstudio	1.1.463	Other	Sapelo2
Ruby	2.5.0	Programming	Sapelo2
runBNG	1.03	Bioinformatics	Sapelo2
Sage	8.0	Other	Sapelo2
Salmon	0.8.2, 0.10.2, 0.13.1	Bioinformatics	Sapelo2
SALSA	2.0	Bioinformatics	Sapelo2
sambamba	0.6.6, 0.6.9	Bioinformatics	Sapelo2
samblaster	0.1.24	Bioinformatics	Sapelo2
SAMtools	0.1.19, 1.1, 1.3.1, 1.6, 1.9	Bioinformatics	Sapelo2
SAMtools	1.6, 1.3.1, 0.1.19	Bioinformatics	Teaching
SANN	20190528	Bioinformatics	Sapelo2
sbt	1.1.1	Programming	Sapelo2
scala	2.12.4	Programming	Sapelo2
scikit-image	0.13.1, 0.14.0	Other	Sapelo2
SCons	2.5.0	Other	Sapelo2
SCOTCH	6.0.4	Other	Sapelo2
seaview	4.7	Bioinformatics	Sapelo2
Seq-Gen	1.3.4	Bioinformatics	Sapelo2
SeqKit	0.10.1	Bioinformatics	Sapelo2
seqqs	20140225	Bioinformatics	Sapelo2
seqtk	1.2	Bioinformatics	Sapelo2
SGA	0.10.15	Bioinformatics	Sapelo2
shapeit	v2.r904	Bioinformatics	Sapelo2
ShortStack	3.8.5	Bioinformatics	Sapelo2
SICER	1.1	Bioinformatics	Sapelo2
SICERpy	0.1	Bioinformatics	Sapelo2
Sickle	1.33	Bioinformatics	Sapelo2
SignalP	4.1f	Bioinformatics	Sapelo2
Silix	1.2.9	Bioinformatics	Sapelo2
SimLoRD	1.0.2	Bioinformatics	Sapelo2
SINE_Scan	1.1.1	Bioinformatics	Sapelo2
slda	0.1.6	Other	Sapelo2
smoke	4.5	Other	Sapelo2
SMRTLINK	5.1.0.26412, 6.0.0.47841	Bioinformatics	Sapelo2
SMRTLINK	5.0.1.9585, 5.1.0.26412	Bioinformatics	Teaching
Snakemake	5.2.4	Bioinformatics	Sapelo2
SNAP-Zoe	20060728	Bioinformatics	Sapelo2
SNAP-Zoe	20060728	Bioinformatics	Teaching
Sniffles	1.0.8	Bioinformatics	Sapelo2
SnoReport	2.0	Bioinformatics	Sapelo2
SNP-ML	1.3.0	Bioinformatics	Sapelo2
snpEff	4.3t	Bioinformatics	Sapelo2
SnpEff	4.3t	Bioinformatics	Teaching
SNPhylo	20160204	Bioinformatics	Sapelo2
SOAPaligner	2.21	Bioinformatics	Sapelo2
SOAPdenovo2	r240	Bioinformatics	Sapelo2
SOAPdenovo2	r240	Bioinformatics	Teaching
SOP-GPU	20180404	Bioinformatics	Sapelo2
SortMeRNA	2.1, 3.0.3	Bioinformatics	Sapelo2
SoX	14.4.2	Other	Sapelo2
SPAdes	3.11.1, 3.12.0	Bioinformatics	Sapelo2
SPAdes	3.11.1	Bioinformatics	Teaching
spams	2.6.1	Other	Sapelo2
Spanki	0.5.1	Bioinformatics	Sapelo2
Spark	2.2.1	Other	Sapelo2
SpliceGrapher	0.2.5	Bioinformatics	Sapelo2
SPM	12	Other	Sapelo2
SRAToolKit	2.8.2-1, 2.9.1	Bioinformatics	Sapelo2
sRNAWorkbench	4.5	Bioinformatics	Sapelo2
SSAHA2	2.5.5	Bioinformatics	Sapelo2
SSPACE-longread	1-1	Bioinformatics	Teaching
SSPACE-STANDARD	3.0	Bioinformatics	Teaching
SSPACE	2.1.1	Bioinformatics	Sapelo2
Stacks	1.48, 2.2, 2.3, 2.3b, 2.3d, 2.3e	Bioinformatics	Sapelo2
Stacks	2.0, 1.48	Bioinformatics	Teaching
Stampy	1.0.31	Bioinformatics	Sapelo2
STAR-Fusion	1.5.0	Bioinformatics	Sapelo2
STAR	2.5.3a, 2.6.0c, 2.6.1c	Bioinformatics	Sapelo2
STAR	2.5.3a, 2.6.0c	Bioinformatics	Teaching
StrAuto	1.0	Bioinformatics	Sapelo2
StringTie	1.3.3, 1.3.4d	Bioinformatics	Sapelo2
StringTie	1.3.3, 1.3.4d	Bioinformatics	Teaching
Structure	2.3.4	Bioinformatics	Sapelo2
Structure	2.3.4	Bioinformatics	Teaching
Subread	1.6.2	Bioinformatics	Sapelo2
SUNTANS	20180305	Other	Sapelo2
Supernova	2.0.1, 2.1.1	Bioinformatics	Sapelo2
SVDetect	0.7	Bioinformatics	Sapelo2
SWIG	3.0.12	Bioinformatics	Sapelo2
Synima	20181205	Bioinformatics	Sapelo2
Tabix	0.2.6	Bioinformatics	Sapelo2
TASSEL	5.2.44	Bioinformatics	Sapelo2
Tbl2asn	04172018	Bioinformatics	Sapelo2
TCSF_IMRA	1.3	Bioinformatics	Sapelo2
TensorFlow-models	20180620	Other	Sapelo2
TensorFlow	1.8.0, 1.10.1	Other	Sapelo2
Theano	0.9.0, 1.0.2	Other	Sapelo2
TigMint	1.1.2	Bioinformatics	Sapelo2
TMHMM	2.0c	Bioinformatics	Sapelo2
Tophat	2.1.0, 2.1.1	Bioinformatics	Sapelo2
TopHat	2.1.1	Bioinformatics	Teaching
TPP	5.1.0	Bioinformatics	Sapelo2
TransDecoder	2.1.0	Bioinformatics	Sapelo2
Transposome	0.12.1	Bioinformatics	Sapelo2
TrimAl	1.4.1	Bioinformatics	Sapelo2
Trimmomatic	0.36	Bioinformatics	Sapelo2
Trimmomatic	0.36	Bioinformatics	Teaching
Trim_Galore	0.4.5	Bioinformatics	Sapelo2
Trinity	r20140717, 2.5.1, 2.6.6, 2.8.4	Bioinformatics	Sapelo2
Trinity	2.6.6	Bioinformatics	Teaching
Trinotate	3.1.1	Bioinformatics	Sapelo2
TRNAscan-SE	2.0.0	Bioinformatics	Sapelo2
UCLUST	1.2.22q	Bioinformatics	Sapelo2
ucsc	359	Bioinformatics	Sapelo2
UPP	3.2	Other	Sapelo2
USEARCH	10.0.240	Bioinformatics	Sapelo2
VarScan	2.4.2	Bioinformatics	Sapelo2
VCF-kit	0.1.6	Bioinformatics	Sapelo2
vcf2diploid	0.2.6a	Chemistry	Sapelo2
vcf2phylip	1.5	Bioinformatics	Sapelo2
vcflib	20180410	Bioinformatics	Sapelo2
VCFtools	0.1.15	Bioinformatics	Sapelo2
VCFtools	0.1.15	Bioinformatics	Teaching
Velvet	1.2.10	Bioinformatics	Sapelo2
Velvet	1.2.10	Bioinformatics	Teaching
VelvetOptimiser	2.2.5, 2.2.6	Bioinformatics	Sapelo2
ViennaRNA	2.4.3, 2.4.6	Bioinformatics	Sapelo2
Vmatch	2.3.0	Bioinformatics	Sapelo2
VSEARCH	2.8.1	Bioinformatics	Sapelo2
WGS	8.3rc2	Bioinformatics	Sapelo2
WebLogo	3.6.0	Bioinformatics	Sapelo2
WEKA	3.8.3	Other	Sapelo2
WPS	3.8	Other	Sapelo2
WPS	3.8	Other	Teaching
WRF-Chem	3.6.1, 3.8.0	Other	Sapelo2
WRF-Fire	20170221	Other	Sapelo2
WRF	3.6.1, 3.8.0	Other	Sapelo2
WRF	3.8	Other	Teaching
WRFDA	3.8	Other	Teaching
WU Blast	2.2.6	Bioinformatics	Sapelo2
xforms	1.2.4	Graphics	Sapelo2
YASRA	2.33	Bioinformatics	Sapelo2

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 | [[GARLI-Sapelo2|GARLI]] || 2.01 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
 |-
-| [[GATK-Sapelo2|GATK]] || 3.4-0, 3.8-0, 3.8-1, 4.0.3.0, 4.0.11.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
+| [[GATK-Sapelo2|GATK]] || 3.4-0, 3.8-0, 3.8-1, 4.0.3.0, 4.0.11.0, 4.1.0.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
 |-
 | [[GATK-Teaching|GATK]] || 3.8-0, 3.4-0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]

Software-old: Difference between revisions

Revision as of 13:58, 9 July 2019

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