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Cell.pdf Cell Mar 8 Mar 8 2.4 MB 15  
J. Bacteriol.pdf Journal of Bacteriol Mar 8 Mar 8 6.8 MB 16  
PerM4_Mac64.tar.gz PerM 0.4.0 Mac OS/Intel   Featured Feb 21 Feb 21 166 KB 8  
PerM4_Win32.zip PerM version 4.0 OpenMP for Win32   Featured Feb 21 Feb 21 175 KB 13  
PerM4Source.tar.gz PerM version 4.0 Source   Featured Feb 21 Feb 21 111 KB 36  
PerM4_Linux64(noOpenMp).gz PerM version 4.0 without OpenMP   Featured Feb 21 Feb 21 2.1 MB 34  
PerM4_Linux64.gz PerM version 4.0 OpenMP   Featured Feb 21 Feb 21 2.1 MB 48  
perm PerM 0.3.9 Mac OS/Intel Jan 13 Jan 13 467 KB 10  
PerM3.9Source.tar.gz PerM 0.3.9 Source Updated Dec 28 Dec 28 107 KB 26  
PerM3.9Linux64WithOpenMp.gz PerM 0.3.9 With OpenMp Nov 28 Nov 28 2.1 MB 44  
permWin32(NoOpenMP)3.9.zip PerM 0.3.9 (Win32-bit) (No openMp) Nov 26 Nov 26 170 KB 6  
PerM3.9Linux64(noOpenMp).gz PerM 0.3.9 (64-bit) (No openMp) Nov 20 Nov 20 2.1 MB 42  
PerM_Win32(No openMP)_3.6.zip PerM 3.6 for win32 (No OpenMP) Oct 2011 Oct 2011 1.0 MB 14  
sampleReadsDatas.zip Sample Reads data   Featured Oct 2011 Oct 2011 1.8 MB 57  
PerM_3.6_Source.tar.gz PerM 0.3.6 Source (Fixed issue 46 to deal 'n') Jul 2011 Jul 2011 101 KB 146  
PerM_Linux64(noOpenMp)_0.3.6.gz PerM 3.6 (Fixed issue 46 to deal 'n') (No-OpenMp) Jul 2011 Jul 2011 2.1 MB 25  
PerM_Linux64_0.3.6.gz PerM 3.6 (Fixed issue 46 to deal 'n') Jul 2011 Jul 2011 2.1 MB 130  
PerM_Linux64_0.3.5(noOpenMp).gz PerM 3.5 executable (No openMP) May 2011 May 2011 2.1 MB 14  
PerM_0.3.5_Source.tar.gz PerM Source May 2011 May 2011 101 KB 21  
PerM0.3.5_Linux64.gz PerM 3.5 May 2011 May 2011 2.0 MB 33  
PerM0.3.3_Linux64.gz PerM version 0.3.3 OpenMp 64bit (fix minor issue 37, 40, 41) Feb 2011 Feb 2011 2.1 MB 279  
PerM0.3.3_Linux64(noOpenMp).gz PerM version 0.3.3 with no openMp 64bit (fix minor issue 37, 40, 41) Feb 2011 Feb 2011 2.1 MB 37  
PerM0.3.3Source.zip PerM version 0.3.3 Source (fix minor issue 37, 40, 41) Feb 2011 Feb 2011 135 KB 114  
PerM3.2Source.zip PErM source 0.3.2 Dec 2010 Dec 2010 134 KB 38  
PerM3.2Linux64(noOpenMp).gz PerM version 0.3.2 (fix segmentation fault on -k 2 or - k -1 and -a) with no openMP Dec 2010 Dec 2010 2.1 MB 25  
PerM3.2Linux64.gz PerM version 0.3.2 (fix segmentation fault on -k 2 or - k -1 and -a) Dec 2010 Dec 2010 2.1 MB 26  
PerM_Linux64_0.3.1_(noOpenMp).gz PerM version 0.3.1 (fix .mapping output format for fasta input)(No OpenMp) Oct 2010 2.1 MB 29  
PerM_0.3.1_Linux64.gz PerM version 0.3.1 (fix .mapping output format for fasta input) Oct 2010 2.1 MB 43  
PerM0.3.1Source.zip PerM version 0.3.1 (fix .mapping output format for fasta input) Oct 2010 132 KB 48  
PerMSource3.0.zip PerM version 3.0 Source (fix many small issues) Sep 2010 125 KB 21  
PerM_Linux64(noOpenMp).gz PerM version 3.0 (fix many small issues) (No openMP) Sep 2010 2.1 MB 84  
PerM_Linux64.gz PerM version 3.0 (fix many small issues) Sep 2010 2.1 MB 29  
qPerM.tar.gz qPerM: Shell wrapper which parallelizes the mapping of a single read set   Featured Sep 2010 227 KB 50  
iPerM.tar.gz iPerM: Shell wrapper to reduce memory requirement by splitting mapping   Featured Sep 2010 4.9 KB 49  
PerMStats.sh Bash script to process mapping log for multiple read set   Featured Jul 2010 2.3 KB 122  
PerMSource0.2.9.9.zip PerM 0.2.9.9 Source (Can be full sensitive to 8 for 100bp Illumina read. Fixed problem for long odd-length Read) Jul 2010 127 KB 34  
DefensePowerPoint.zip Defense PowerPoint for PerM and Clippers (Change Font Courier to Courier new if distortion)   Featured Jul 2010 930 KB 254  
PerM_Linux64_0.2.9.7.gz PerM 0.2.9.7 (Fix -t truncated prefix for SOLiD) Jun 2010 2.1 MB 25  
PerM_Linux64(noOpenMp)0.2.9.7.gz PerM executable for Linux 64 no openmp version 0.2.9.7 (Fixed -t options for SOLiD) Jun 2010 2.0 MB 12  
PerMSource0.2.9.7.zip PerM Source 0.2.9.7 (Fix -t truncated prefix for SOLiD) Jun 2010 127 KB 19  
PerM_Linux64v0.2.9.6.gz PerM executable for Linux 64 wiht openmp version 0.2.9.6 (Fixed long reads -A sensitivity) Jun 2010 2.1 MB 9  
PerM_Linux64_noOpenMp_v0.2.9.6.gz PerM executable for Linux 64 no openmp version 0.2.9.6 (Fixed -A long reads sensitivity) Jun 2010 2.0 MB 6  
PerM_Linux32_v0.2.9.6.gz PerM executable for Linux 32 openmp version 0.2.9.6 (Fixed -A long reads sensitivity) Jun 2010 2.0 MB 32  
PerM_Linux32_noOpenMp_v0.2.9.6.gz PerM executable for Linux 32 no openmp version 0.2.9.6 (Fixed long reads -A sensitivity) Jun 2010 1.9 MB 5  
qPerM.zip qPerM: PerM's wrapper, which map a single read set in parallel Jun 2010 224 KB 43  
Soure0.2.9.4.tar.gz PerM version 0.2.9.4 Source (Fixed issue 25, 26) May 2010 96.9 KB 18  
PerM_Linux64_v0.2.9.4.gz PerM executable for Linux 64 openmp version 0.2.9.4 (Fixed issue 25, 26) May 2010 2.1 MB 23  
PerM_Linux32_v0.2.9.4.gz PerM executable for Linux 32 openmp version 0.2.9.4 (Fixed issue 25, 26) May 2010 2.0 MB 16  
PerM_Linux64_noOpenMp_v0.2.9.4.gz PerM executable for Linux 64 no openmp version 0.2.9.4 (Fixed issue 25, 26) May 2010 2.0 MB 7  
PerM_Linux32_noOpenMp_v0.2.9.4.gz PerM executable for Linux 32 no openmp version 0.2.9.4 (Fixed issue 25, 26) May 2010 1.9 MB 5  
PerMv0.2.9.3forMac.gz PerM (0.2.9.3) executable for mac with no open MP May 2010 126 KB 61  
PerM_Linux32_noOpenMp_v2.9.3.gz PerM executable for Linux 32 no openmp version 0.2.9.3 (Fixed -v option bug limited to 3 mis) May 2010 663 KB 8  
PerM_Linux64(noOpenMp)_v2.9.3.gz PerM executable for Linux 64 no openmp version 0.2.9.3 (Fixed -v option bug limited to 3 mis) May 2010 680 KB 7  
PerM_Linux32_v2.9.3.gz PerM executable for Linux 32 with openmp version 0.2.9.3 May 2010 664 KB 10  
PerM_Linux64_v2.9.3.gz PerM executable for Linux 64 with openmp version 0.2.9.3 May 2010 680 KB 12  
SourceV2.9.3.tar.gz PerM Source 0.2.9.3 Fix -v option bug which use allow only 3 mis May 2010 92.9 KB 13  
PerM_Linux64_v0.2.9.2.gz PerM executable for Linux 64 with openmp version 0.2.9.2 (Fixed -v option which limited to only 3 mis) May 2010 680 KB 4  
PerM_Linux32_v0.2.9.2.gz PerM executable for Linux 32 with openmp version 0.2.9.1 May 2010 663 KB 4  
PerM_Linux64(noOpenMp)_v0.2.9.2.gz PerM executable for Linux 64 no openmp version 0.2.9.2 (Fixed -v option bug limited to 3 mis) May 2010 679 KB 4  
PerM_0.2.9.2_Source.tar.gz PerM Source 0.2.9.2 Fix -v option bug which use allow only 3 mis May 2010 778 KB 5  
PerM_Linux32_noOpenMp_v0.2.9.2.gz PerM executable for Linux 32 no openmp version 0.2.9.2 (Fixed -v option bug limited to 3 mis) May 2010 662 KB 5  
PerM_Linux64_NoOpenMp.gz PerM 0.2.8 for Linux 64 bit (For system with no OpenMp support) Apr 2010 657 KB 37  
Source_v0.2.8.zip PerM 0.2.8 source compilable for Linux, Windows and Mac Apr 2010 116 KB 39  
PerM(Linux64)v0.2.8.gz PerM 0.2.8 for Linux 64 (New Seed F0 and F1 with shorter mappable length) Apr 2010 659 KB 27  
PerM_Linux32_NoOpenMp.gz PerM 0.2.8 for Linux 32 bit (For system with no OpenMp support) Apr 2010 642 KB 19  
PerM(Linux32)v0.2.8.gz PerM 0.2.8 for Linux 32 bit (New Seed F0 and F1 with shorter mappable length) Apr 2010 643 KB 10  
pileUp.sh The samtools bash shell wrapper for getting the expression level bed files. Apr 2010 1.6 KB 87  
Wig2Bed.py python scripts to translate wig(gle) format to the condensed bed format.   Wig UCSCgenomebrowser Apr 2010 2.5 KB 123  
PerM_Linux32bits(noOpenMp).gz PerM version 0.2.6 for Linux 32-bit PC without OpenMP (add CS CQ column in sam output) Mar 2010 638 KB 13  
PerM_Linux64bits(noOpenMp).gz PerM version 0.2.6 for Linux 64-bit PC without OpenMP (add CS CQ column in sam output) Mar 2010 653 KB 17  
PerM(Linux64bits).gz PerM version 0.2.6 for Linux 64-bit PC with OpenMP (add CS CQ column in paired SOLiD sam ouput) Mar 2010 655 KB 35  
PerM(Linux32bits).gz PerM version 0.2.6 for Linux 32-bit PC with OpenMP (add CS CQ column in paired SOLiD sam output) Mar 2010 640 KB 158  
Source_0.2.6.zip Version 0.2.6 Source code (add CS CQ column in sam for paired end SOLiD read) Mar 2010 119 KB 20  
PerM(MacWithOpenMP).tgz PerM version 0.2.5 for Mac (Apple) copmuter with OpenMP (fixed index path string) Mar 2010 135 KB 23  
Source_code_0.2.5.zip Source code 0.2.5 (Fixed incorrect multi-mapped reads count and index path) Mar 2010 119 KB 12  
PerM(inux32).gz PerM version 0.2.5 for Linux 32-bit PC with OpenMP (fixed index path string) Feb 2010 638 KB 19  
PerM_Linux32(noOpenMp).gz PerM version 0.2.5 for Linux 32-bit PC without OpenMP (fixed index path string) Feb 2010 636 KB 17  
PerM(Linux64).gz PerM version 0.2.5 for Linux 64-bit PC with OpenMP (fixed index path string) Feb 2010 653 KB 28  
PerM_Win32.zip PerM Exe for Windows (windows 7, vista, xp for both 32 and 64 bit) Feb 2010 66.8 KB 48  
SourceCode_0.2.4.zip Source code 0.2.4 (Fixed incorrect multi-mapped reads count and index path) Feb 2010 118 KB 16  
PerM_Linux32.zip Version 0.2.3 for Linux 32-bit PC Feb 2010 637 KB 19  
PerM_Linux64.zip Version 0.2.3 for Linux 64-bit PC Feb 2010 651 KB 50  
PerMStat.sh Bash/R script to sum the mapping count for stdout log after PerM verstion 0.2.3. Feb 2010 1.9 KB 208  
SourceCode_0.2.3.zip Source code 0.2.3 (Fixed incorrect multi-mapped reads count bug) Feb 2010 115 KB 12  
PerM_Linux64_v0.2.3.zip PerM version 0.2.3 for Linux 64-bit PC (Fixed incorrect multi-mapped reads count in -E mode) Feb 2010 650 KB 18  
PerM_0.2.3_source.zip Source code 0.2.3 (Fixed incorrect multi-mapped reads count problem) Feb 2010 115 KB 12  
Source_Code_PerM_0.2.2.zip v 0.2.2 with OpenMP (Fixed reads filtering problem for pair-end reads) Feb 2010 115 KB 12  
PerM_Win64.zip PerM exe on Windows 64 with OpenMP Dec 2009 75.1 KB 24  
Source_Code_PerM_0.2.1.zip v 0.2.1, updated from 0.2.0 to make it compilable on VC 2008 with OpenMP Dec 2009 757 KB 25  
MVFmaker_NewFormat.txt MVFmaker_NewFormat   Configuration Dec 2009 244 bytes 69  
PerM_Win32_without_openMP.zip PerM exeutable 2.0 (WinXP 32 bit PC with no OpenMP) Dec 2009 276 KB 26  
PerM_Win64_without_openMP.zip PerM exe on Windows 7, 64 bit with no OpenMP Dec 2009 267 KB 12  
PowerPoint.zip Slides (Must open with Powerpoints 2003) Dec 2009 500 KB 66  
PerM_Linux64_without_openMP.zip PerM version 0.2.0 for Linux 64-bit PC WITHOUT openMP support Dec 2009 640 KB 25  
Source_Code _PerM_0.2.0.zip Source code PerM version 0.2.0 (with makefile for OpenMp) Dec 2009 110 KB 15  
PerM_0.2.0.zip The Source Code of PerM 2.0 (Fixed Slow Problem for transcriptom long Illumina reads) Dec 2009 112 KB 17  
PerM_noOpenMP PerM exeutable 2.0 Red Hat No OpenMP Dec 2009 1.7 MB 19  
PerM PerM exeutable 2.0 for Red Hat 64-bit with OpenMP Dec 2009 1.7 MB 58  
PerM_noMP Complied PerM without openMP for 64-bit linux (red hat) 0.1.5 version Nov 2009 1.6 MB 167  
PerM_0.1.5.zip PerM 0.1.5 GCC (command line only, makefile updated) Nov 2009 724 KB 29  
  
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