Deletion log

Below is a list of the most recent deletions.

• 13:32, 11 May 2026 Shtsai talk contribs deleted page PartitionFinder2-Sapelo2 (content before blanking was: "Category:Sapelo2Category:SoftwareCategory:Bioinformatics === Category === Bioinformatics === Program On === Sapelo2 === Version === 2.1.1 === Author / Distributor === Details at [http://www.robertlanfear.com/partitionfinder/ partitionfinder] === Description === "PartitionFinder is free open source software to select best-fit partitioning schemes and models of molecular evolution for phylogenetic analyses." More detailes are at [http://...")
• 14:45, 6 May 2026 Shtsai talk contribs deleted page System Administration (content was: "== Introduction == System administration at GACRC requires experience and advanced knowledge managing the Linux operating system as well the ability to quickly and accurately troubleshoot, configure and plan the automated clustering of many nodes with little or no manual intervention. The cluster platform provides a fundamental environment f...", and the only contributor was "Curtis E. Combs Jr." (talk))
• 14:23, 6 May 2026 Shtsai talk contribs deleted page CategorySearch (content was: "<dynamicpagelist> category=Sapelo order=ascending ordermethod=lastedit shownamespace=false </dynamicpagelist>", and the only contributor was "Raj76" (talk))
• 13:36, 6 May 2026 Shtsai talk contribs deleted page Troubleshooting (content was: "==Introduction== This page provides the common errors and solutions for jobs at GACRC cluster. The examples are made from Sapelo2 environment, but the solutions apply to Linux clusters as well. ==File format== The text files, such as submission script, fasta file or other text data files at Linux should be in ASCII format. If the files are generated under other operating system or copied from the web, there could introduce hidden characters which cannot be recognized by L...")
• 13:34, 6 May 2026 Shtsai talk contribs deleted page Best Practices on Sapelo (content was: " Data management workflow ")
• 13:32, 6 May 2026 Shtsai talk contribs deleted page YH-T-Template (content was: "Category:TeachingCategory:Software[[Category:<!-- CATEGORY3 BEGIN --> Bioinformatics <!-- CATEGORY3 END -->]] === Category === <!-- CATEGORY3 BEGIN --> Bioinformatics <!-- CATEGORY3 END --> === Program On === Teaching === Version === <!-- VERSION BEGIN -->2.0.6<!-- VERSION END --> === Author / Distributor === <!-- HOME_URL BEGIN --> [http://trinityrnaseq.sourcefor...", and the only contributor was "Yhuang" (talk))
• 13:31, 6 May 2026 Shtsai talk contribs deleted page Trinity-Teaching (content was: "Category:TeachingCategory:SoftwareCategory:Bioinformatics === Category === Bioinformatics === Program On === Teaching === Version === 2.6.6 === Author / Distributor === [http://trinityrnaseq.github.io Trinity] === Description === "Trinity represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data. Trini...", and the only contributor was "Yhuang" (talk))
• 13:31, 6 May 2026 Shtsai talk contribs deleted page YH-S2-Template (content was: "Category:Sapelo2Category:Software[[Category:<!-- CATEGORY3 BEGIN --> Bioinformatics <!-- CATEGORY3 END -->]] === Category === <!-- CATEGORY3 BEGIN --> Bioinformatics <!-- CATEGORY3 END --> === Program On === Sapelo2 === Version === <!-- VERSION BEGIN -->2.0.6<!-- VERSION END --> === Author / Distributor === <!-- HOME_URL BEGIN --> [http://trinityrnaseq.sourceforge...", and the only contributor was "Yhuang" (talk))
• 13:31, 6 May 2026 Shtsai talk contribs deleted page Trimmomatic-Teaching (content was: "Category:TeachingCategory:SoftwareCategory:Bioinformatics === Category === Bioinformatics === Program On === Teaching === Version === 0.36 === Author / Distributor === [http://www.usadellab.org/cms/?page=trimmomatic Trimmomatic] === Description === "Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.The se...", and the only contributor was "Yhuang" (talk))
• 13:29, 6 May 2026 Shtsai talk contribs deleted page Software Installed on Sapelo2 (content was: " Once you login into the cluster, you can use LMOD commands to check if an application is installed. To display all module files installed, use <pre class="gcommand"> ml avail </pre> To search for a given package, use <pre class="gcommand"> ml spider appsname </pre> where ''appsname'' needs to be replaced by the application name (or portions of it) that you wish to search for...", and the only contributor was "Shtsai" (talk))
• 13:29, 6 May 2026 Shtsai talk contribs deleted page Test-software-page (content was: "Category:Sapelo2Category:SoftwareCategory:Chemistry === Category === Chemistry === Program On === Sapelo2 === Version === 3Mar2020 === Author / Distributor === Please see http://lammps.sandia.gov/authors.html === Description === From http://lammps.sandia.gov/ : "LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecul...", and the only contributor was "Shtsai" (talk))
• 13:28, 6 May 2026 Shtsai talk contribs deleted page TopHat-Teaching (content was: "Category:TeachingCategory:SoftwareCategory:Bioinformatics === Category === Bioinformatics === Program On === Teaching === Version === 2.1.1 === Author / Distributor === [http://ccb.jhu.edu/software/tophat/ TopHat] === Description === "TopHat is a fast splice junction mapper for RNA-Seq reads." More details are at [http://ccb.jhu.edu/software/tophat/ TopHat]...", and the only contributor was "Yhuang" (talk))
• 13:28, 6 May 2026 Shtsai talk contribs deleted page SSPACE-longread-Teaching (content was: "Category:TeachingCategory:SoftwareCategory:Bioinformatics === Category === Bioinformatics === Program On === Teaching === Version === 1-1 === Author / Distributor === [https://www.baseclear.com/services/bioinformatics/basetools/sspace-longread/ SSPACE-longread] === Description === "SSPACE-LongRead is a stand-alone program for scaffolding pre-assembled contig...", and the only contributor was "Yhuang" (talk))
• 13:28, 6 May 2026 Shtsai talk contribs deleted page SSPACE-STANDARD-Teaching (content was: "Category:TeachingCategory:SoftwareCategory:Bioinformatics === Category === Bioinformatics === Program On === Teaching === Version === 3.0 === Author / Distributor === [https://www.baseclear.com/services/bioinformatics/basetools/sspace-standard/ SSPACE-STANDARD] === Description === " SSPACE-standard is a stand-alone program for scaffolding pre-assembled conti...", and the only contributor was "Yhuang" (talk))
• 13:27, 6 May 2026 Shtsai talk contribs deleted page WRFDA-Teaching (content was: "Category:TeachingCategory:SoftwareCategory:Other === Category === Other === Program On === Teaching === Version === 3.8 === Author / Distributor === Please see http://www2.mmm.ucar.edu/wrf/users/wrfda/index.html === Description === From http://www2.mmm.ucar.edu/wrf/users/wrfda/index.html: "The WRFDA system is in the public domain and is freely availab...", and the only contributor was "Shtsai" (talk))
• 13:27, 6 May 2026 Shtsai talk contribs deleted page Velvet-Teaching (content was: "Category:TeachingCategory:SoftwareCategory:Bioinformatics === Category === Bioinformatics === Program On === Teaching === Version === 1.2.10 === Author / Distributor === [http://www.ebi.ac.uk/~zerbino/velvet/ Velvet] === Description === "Sequence assembler for very short reads" More details are at [http://www.ebi.ac.uk/~zerbino/velvet/ Velvet] === Running P...", and the only contributor was "Yhuang" (talk))
• 13:26, 6 May 2026 Shtsai talk contribs deleted page TMHMMGuide (content was: "<pre> TMHMM2.0 User's guide This program is for prediction of transmembrane helices in proteins. July 2001: TMHMM has been rated best in an independent comparison of programs for prediction of TM helices: S. Moller, M.D.R. Croning, R. Apweiler. Evaluation of methods for the prediction of membrane spanning regions. Bioinformatics, 17(7):646-653, July 2001. (medline) Quot...", and the only contributor was "Yhuang" (talk))
• 13:24, 6 May 2026 Shtsai talk contribs deleted page Smoke-Sapelo2 (content was: "Category:Sapelo2Category:SoftwareCategory:Other === Category === Other === Program On === Sapelo2 === Version === 4.7 ===Author / Distributor=== Please see https://www.cmascenter.org/smoke/ ===Description=== From https://www.cmascenter.org/smoke/: "SMOKE is an active open-source development project supported and distributed by the CEMPD through the Community Modelin...", and the only contributor was "Shtsai" (talk))
• 13:24, 6 May 2026 Shtsai talk contribs deleted page Stacks-Teaching (content was: "Category:TeachingCategory:SoftwareCategory:Bioinformatics === Category === Bioinformatics === Program On === Teaching === Version === 1.48, 2.0 === Author / Distributor === [http://creskolab.uoregon.edu/stacks/ Stacks] === Description === "Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the pur...")
• 13:23, 6 May 2026 Shtsai talk contribs deleted page VCFtools-Teaching (content was: "Category:TeachingCategory:SoftwareCategory:Bioinformatics === Category === Bioinformatics === Program On === Teaching === Version === 0.1.15 === Author / Distributor === [https://vcftools.github.io VCFtools] === Description === "The aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF...", and the only contributor was "Yhuang" (talk))
• 13:23, 6 May 2026 Shtsai talk contribs deleted page Xdot-Teaching (content was: "Category:TeachingCategory:SoftwareCategory:Graphics === Category === Graphics === Program On === Teaching === Version === 1.1 === Author / Distributor === Please see https://github.com/jrfonseca/xdot.py === Description === xdot is an interactive viewer for graphs written in Graphviz's dot language. For more information, please see https://github.com/jrf...", and the only contributor was "Shtsai" (talk))
• 13:22, 6 May 2026 Shtsai talk contribs deleted page Software-old (content was: " 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: <pre class="gcommand"> module spider </pre> You can also use the command above to search for a spec...", and the only contributor was "Ben" (talk))
• 13:22, 6 May 2026 Shtsai talk contribs deleted page RepeatScout-Teaching (content was: "Category:TeachingCategory:SoftwareCategory:Bioinformatics === Category === Bioinformatics === Program On === Teaching === Version === 1.05 === Author / Distributor === [http://bix.ucsd.edu/repeatscout/ RepeatScout] === Description === "The purpose of the RepeatScout software is to identify repeat family sequences from genomes where hand-curated repeat datab...", and the only contributor was "Yhuang" (talk))
• 13:21, 6 May 2026 Shtsai talk contribs deleted page SnpEff-Teaching (content was: "Category:TeachingCategory:SoftwareCategory:Bioinformatics === Category === Bioinformatics === Program On === Teaching === Version === 4.3t === Author / Distributor === [http://sourceforge.net/projects/snpeff/ snpEff] === Description === "SnpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of genetic variants (su...", and the only contributor was "Yhuang" (talk))
• 13:21, 6 May 2026 Shtsai talk contribs deleted page SeqKit-Teaching (content was: "Category:TeachingCategory:SoftwareCategory:Bioinformatics === Category === Bioinformatics === Program On === Teaching === Version === 0.10.2 === Author / Distributor === W Shen. More details at [https://bioinf.shenwei.me/seqkit/ Seqkit] Citation: W Shen, S Le, Y Li*, F Hu*. SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation. PLOS...", and the only contributor was "Shtsai" (talk))
• 13:21, 6 May 2026 Shtsai talk contribs deleted page STAR-Teaching (content was: "Category:TeachingCategory:SoftwareCategory:Bioinformatics === Category === Bioinformatics === Program On === Teaching === Version === 2.6.0c === Author / Distributor === [https://github.com/alexdobin/STAR STAR] === Description === "STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays." More details are at [https://github.com/alexd...", and the only contributor was "Yhuang" (talk))
• 13:21, 6 May 2026 Shtsai talk contribs deleted page SPAdes-Teaching (content was: "Category:TeachingCategory:SoftwareCategory:Bioinformatics === Category === Bioinformatics === Program On === Teaching === Version === 3.11.1 === Author / Distributor === [http://cab.spbu.ru/software/spades/ SPAdes] === Description === "Genome assembler for single-cell and isolates data sets" More details are at [http://cab.spbu.ru/software/spades/ SPAdes] =...", and the only contributor was "Yhuang" (talk))
• 13:21, 6 May 2026 Shtsai talk contribs deleted page SOAPdenovo2-Teaching (content was: "Category:TeachingCategory:SoftwareCategory:Bioinformatics === Category === Bioinformatics === Program On === Teaching === Version === r240 === Author / Distributor === [http://soap.genomics.org.cn/index.html SOAPdenovo2] === Description === "SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for human-sized genomes. Th...", and the only contributor was "Yhuang" (talk))
• 13:20, 6 May 2026 Shtsai talk contribs deleted page SNAP-Zoe-Teaching (content was: "Category:TeachingCategory:SoftwareCategory:Bioinformatics === Category === Bioinformatics === Program On === Teaching === Version === 20060728 === Author / Distributor === [https://github.com/KorfLab/SNAP SNAP-Zoe] === Description === "SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. SNAP is an acroynm for...", and the only contributor was "Yhuang" (talk))
• 13:20, 6 May 2026 Shtsai talk contribs deleted page PartitionFinder-Teaching (content was: "Category:TeachingCategory:SoftwareCategory:Bioinformatics === Category === Bioinformatics === Program On === Teaching === Version === 2.1.1 === Author / Distributor === Details are at [http://www.robertlanfear.com/partitionfinder/ Partitionfinder] === Description === "PartitionFinder is free open source software to select best-fit partitioning schemes a...", and the only contributor was "Shtsai" (talk))
• 13:20, 6 May 2026 Shtsai talk contribs deleted page PASTA-Teaching (content was: "Category:TeachingCategory:SoftwareCategory:Bioinformatics === Category === Bioinformatics === Program On === Teaching === Version === 1.8.2 ===Author / Distributor=== [https://github.com/smirarab/pasta] ===Description=== PASTA (Practical Alignment using SATe and Transitivity). === Running Program === Also refer to Running Jobs on the teaching cluster...", and the only contributor was "Pakala" (talk))
• 13:19, 6 May 2026 Shtsai talk contribs deleted page RepeatModeler-Teaching (content was: "Category:TeachingCategory:SoftwareCategory:Bioinformatics === Category === Bioinformatics === Program On === Teaching === Version === 1.0.11 === Author / Distributor === [http://www.repeatmasker.org/RepeatModeler/ RepeatModeler] === Description === "RepeatModeler is a de-novo repeat family identification and modeling package. At the heart of RepeatModeler a...", and the only contributor was "Yhuang" (talk))
• 13:19, 6 May 2026 Shtsai talk contribs deleted page SMRTLINK-Teaching (content was: "Category:TeachingCategory:SoftwareCategory:Bioinformatics === Category === Bioinformatics === Program On === Teaching === Version === 5.1.0.26412 === Author / Distributor === [https://www.pacb.com/support/software-downloads SMRTLINK] === Description === "PacBio open-source SMRT Analysis software suite is designed for use with Single Molecule, Real-Time (SMRT...", and the only contributor was "Yhuang" (talk))
• 13:19, 6 May 2026 Shtsai talk contribs deleted page QIIME2-Teaching (content was: "Category:TeachingCategory:SoftwareCategory:Bioinformatics === Category === Bioinformatics === Program On === Teaching === Version === 2018.6, 2018.8 === Author / Distributor === [http://qiime2.org/ QIIME2] === Description === "QIIME is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data." More details are a...", and the only contributor was "Yhuang" (talk))
• 13:19, 6 May 2026 Shtsai talk contribs deleted page RepeatMasker-Teaching (content was: "Category:TeachingCategory:SoftwareCategory:Bioinformatics === Category === Bioinformatics === Program On === Teaching === Version === 4.0.7 === Author / Distributor === [http://www.repeatmasker.org/ RepeatMasker] === Description === "RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of...", and the only contributor was "Yhuang" (talk))
• 13:18, 6 May 2026 Shtsai talk contribs deleted page OOD Apps: Files (content was: "OnDemand provides a web-based File Explorer that can be used to upload and download files to your OSC home directory or project directory, and copy, delete, rename, and edit files. <s>Here is a tutorial video that gives a overview of OnDemand's file management client's capabilities and how to utilize them:</s> <s>Here you can see a screen shot of what the main inter...", and the only contributor was "Bcarpenter" (talk))
• 13:18, 6 May 2026 Shtsai talk contribs deleted page Pilon-Teaching (content was: "Category:TeachingCategory:SoftwareCategory:Bioinformatics === Category === Bioinformatics === Program On === Teaching === Version === 1.22 === Author / Distributor === [https://github.com/broadinstitute/pilon/wiki pilon] === Description === "Pilon is a software tool which can be used to: (i) Automatically improve draft assemblies, (ii)Find variation among st...", and the only contributor was "Yhuang" (talk))
• 13:17, 6 May 2026 Shtsai talk contribs deleted page Pynini-Teaching (content was: "Category:TeachingCategory:SoftwareCategory:Other === Category === Other === Program On === Teaching === Version === 2.0.8 === Author / Distributor === Please see http://www.openfst.org/twiki/bin/view/GRM/Pynini === Description === From http://www.openfst.org/twiki/bin/view/GRM/Pynini: "OpenGrm Pynini: Finite-state grammar development in Python " === Running...", and the only contributor was "Shtsai" (talk))
• 13:17, 6 May 2026 Shtsai talk contribs deleted page MuTect-Teaching (content was: "Category:TeachingCategory:SoftwareCategory:Bioinformatics === Category === Bioinformatics === Program On === Teaching === Version === 1.1.7 === Author / Distributor === [http://www.broadinstitute.org/cancer/cga/mutect MuTect] === Description === MuTect is a method developed at the Broad Institute for the reliable and accurate identification of somatic...", and the only contributor was "Shtsai" (talk))
• 13:17, 6 May 2026 Shtsai talk contribs deleted page Racon-Teaching (content was: "Category:TeachingCategory:SoftwareCategory:Bioinformatics === Category === Bioinformatics === Program On === Teaching === Version === 1.4.7 ===Author / Distributor=== Please see https://github.com/isovic/racon ===Description=== From https://github.com/isovic/racon: Racon is a "Consensus module for raw de novo DNA assembly of long uncorrected reads. " === R...", and the only contributor was "Shtsai" (talk))
• 13:17, 6 May 2026 Shtsai talk contribs deleted page Minimap2-Teaching (content was: "Category:TeachingCategory:SoftwareCategory:Bioinformatics === Category === Bioinformatics === Program On === Teaching === Version === 2.10, 2.13, 2.17 === Author / Distributor === [https://github.com/lh3/minimap2 minimap2] === Description === "Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference databas...", and the only contributor was "Shtsai" (talk))
• 13:16, 6 May 2026 Shtsai talk contribs deleted page Ms-Teaching (content was: "Category:TeachingCategory:SoftwareCategory:Bioinformatics === Category === Bioinformatics === Program On === Teaching === Version === 20140304 (latest recorded change was made on Mar. 4, 2014.) === Author / Distributor === Richard Hudson === Description === Program to generates samples of gametes. For more information, please see https://uchicago.app.box.com...", and the only contributor was "Shtsai" (talk))
• 13:16, 6 May 2026 Shtsai talk contribs deleted page Pweave-Teaching (content was: "Category:TeachingCategory:SoftwareCategory:Other === Category === Other === Program On === Teaching === Version === 0.30.3 === Author / Distributor === Please see http://mpastell.com/pweave/ === Description === From http://mpastell.com/pweave/: "Pweave is a scientific report generator and a literate programming tool for Python. Pweave can capture the results...", and the only contributor was "Shtsai" (talk))
• 13:16, 6 May 2026 Shtsai talk contribs deleted page Proovread-Teaching (content was: "Category:TeachingCategory:SoftwareCategory:Bioinformatics === Category === Bioinformatics === Program On === Teaching === Version === 2.14.1 === Author / Distributor === [https://github.com/BioInf-Wuerzburg/proovread proovread] === Description === "PacBio hybrid error correction through iterative short read consensus" More details are at [https://github.com/...", and the only contributor was "Yhuang" (talk))
• 13:16, 6 May 2026 Shtsai talk contribs deleted page Prokka-Teaching (content was: "Category:TeachingCategory:SoftwareCategory:Bioinformatics === Category === Bioinformatics === Program On === Teaching === Version === 1.13 === Author / Distributor === [http://www.vicbioinformatics.com/software.prokka.shtml prokka] === Description === "Prokka is a software tool for the rapid annotation of prokaryotic genomes.". More details are at [http://ww...", and the only contributor was "Shtsai" (talk))
• 13:15, 6 May 2026 Shtsai talk contribs deleted page LADR-Teaching (content was: "Category:TeachingCategory:SoftwareCategory:Other === Category === Other === Program On === Teaching === Version === 2009-11A === Author / Distributor === Please see https://www.cs.unm.edu/~mccune/mace4/ === Description === LADR is a command-line version of Prover9, Mace4, and other programs. Prover9 is an automated theorem prover for first-order and equation...", and the only contributor was "Shtsai" (talk))
• 13:15, 6 May 2026 Shtsai talk contribs deleted page Miniasm-Teaching (content was: "Category:TeachingCategory:SoftwareCategory:Bioinformatics === Category === Bioinformatics === Program On === Teaching === Version === 0.3 === Author / Distributor === [https://github.com/lh3/miniasm miniasm] === Description === "Miniasm is a very fast OLC-based de novo assembler for noisy long reads." More details are at [https://github.com/lh3/miniasm miniasm...", and the only contributor was "Shtsai" (talk))
• 13:14, 6 May 2026 Shtsai talk contribs deleted page OrthoFinder-Teaching (content was: "Category:TeachingCategory:SoftwareCategory:Bioinformatics === Category === Bioinformatics === Program On === Teaching === Version === 2.1.2 === Author / Distributor === [https://github.com/davidemms/OrthoFinder OrthoFinder] === Description === "OrthoFinder is a fast, accurate and comprehensive analysis tool for comparative genomics. It finds orthologues and...", and the only contributor was "Yhuang" (talk))
• 13:14, 6 May 2026 Shtsai talk contribs deleted page Picard-Teaching (content was: "Category:TeachingCategory:SoftwareCategory:Bioinformatics === Category === Bioinformatics === Program On === Teaching === Version === 2.16.0 === Author / Distributor === [http://sourceforge.net/projects/picard picard] === Description === "A set of tools (in Java) for working with next generation sequencing data in the BAM format." More details are at [http:/...", and the only contributor was "Yhuang" (talk))
• 13:13, 6 May 2026 Shtsai talk contribs deleted page Megam-Teaching (content was: "Category:TeachingCategory:SoftwareCategory:Other === Category === Other === Program On === Teaching === Version === 0.92 === Author / Distributor === Please see http://users.umiacs.umd.edu/~hal/megam/ === Description === From http://users.umiacs.umd.edu/~hal/megam/: "MEGA Model Optimization Package: Maximum entropy models are very popular, especially in natu...", and the only contributor was "Shtsai" (talk))