Download Sh Bam 11 Master 21 ##BEST##
The Picard command-line tools are provided as a single executable jar file. You can download a zipped package containing the jar file from the Latest Release project page on Github. The file name will be of the format picard-tools-x.y.z.zip.InstallOpen the downloaded package and place the folder containing the jar file in a convenient directory on your hard drive (or server). Unlike C-compiled programs such as Samtools, Picard cannot simply be added to your PATH, so we recommend setting up an environment variable to act as a shortcut.
Download Sh Bam 11 Master 21
Phylogenetic Binning tool Phylogenetic binning tool for paper on "Morphology-based phylogenetic binning of the lichen genera Allographa and Graphis via molecular site wieght calibration" by Simon Berger available for download here tech report PDF and paper File Conversion scripts shell script by Andre Aberer for fasta to phylip conversion
matlab programs by Lowie Li for fasta to phylip and phylip to fasta conversion
Wrapper Scripts Apurva Narechania at the American Museum of Natural history has kindly put togetehr a couple of wrapper scripts for RAxML :-) raxml_launch_serially.sh:A simple shell script that launches one job after the other awaitingfor completion of each job.
raxml_nexusPartConvert.pl:A Perl script that parses a partitioned alignment in Nexus formatwith charsets and produces a partition guide file to be fed to RAxMLwith -q. Preliminary - works with DNA or AA, but not the two togetheryet, so not suitable for mixed-molecule data. Unless the output getsredirected to a file with ">", it will appear on screen.
raxml_wrapper.pl:A Perl script that reads a raxml.config file with common runparameters and executes a directory of Phylip alignment files in batch,then outputs the results in another directory. See the documentationwith "perldoc ./raxml_wrapper.pl".
Guy Leonard at Exeter has updated his wrapper environment called easyRax Alexis has developed a couple of perls scripts A perlscript for computing bootstrap branch lengths with RAxML. This script can be used to perform the following task with RAxML: Given abest-known ML tree, generate a number of Bootstrap replicates and justre-estimate the branch lengths for that given fixed tree topology oneach Bootstrap replicate.
To invoke the script call it as follows: "perl bsBranchLengths.pl alignmentFileName treeFileName numberOfReplicates". Thescript assumes that the RAxML executable is located in the directorywhere you execute it. Otherwise, if RAxML is located in your Linux/Unixpath just replace every occurence of "./raxmlHPC"by "raxmlHPC" in thescript. The bootstrapped trees with branch lengths will be written intoa file called "bsTrees".
This script is intended for use with programs that inferdivergencetime estimates.
A perlscript for finding the best protein substitution model Hereis a little perl-script that will automatically determine thebest-scoring AA substitution model on a fixed starting tree. Notethat raxmlHPC must be in your $PATH for this to work.
For unpartitioned datasets execute it like this: perl ProteinModelSelection.pl alignmentFile.phylip > outfile The outfile will then containthe best-scoring AA model to use with RAxML.
For partitioned datasets execute it like this: perl ProteinModelSelection.pl alignmentFile.phylip partitionData.txt > outfile The outfilewill then contain the best-scoring AA model for every partition.
James Munro has written a Guide to install RAxML on MACs Olaf Bininda-Emonds has written batchRAxML.pl. This nice script by my good colleague from Munich times Olaf Bininda-Emonds provides a wrapper around RAxML to easily analyze a set of data files according to a common set of the search criteria. Also organizes the RAxML output into a set of subdirectories. Frank Kauff has written PYRAXML2. Frank Kauff at University of Kaiserslautern (formerly at Duke University) has written this cool script that reads NEXUS-style data files and prepares the necessary input files and command-line options for RAxML-VI-HPC. You can download the BETA-version here: PYRAXML2 It requires PYTHON and BIOPYTHON to be installed on your computer.
RAxML v7.2.8 alpha release source code available here
RAxML v7.2.7 (alpha) available for download here
RAxML v7.2.6 available for download here and here is a windows executable
RAxML v7.2.5 (alpha) available for download here and here is a windows executable
RAxML v7.2.4(alpha) available for download here
RAxML v7.2.3 (alpha) available for download here
RAxML v7.2.2 available for download here and download windows executable
RAxML v7.2.1 (alpha) available for download here windows executable here
RAxML v7.2.0 (alpha) available for download here
RAxML v7.1.0 (alpha) available for download here
RAxML v7.0.4 available for download here
RAxML v7.0.3 available for download here
Windows executable. Graham Jones has provided a nice PDF on How to run RAxML under XP and Vista.
Mac executable (iMAC)
Mac executable (iMAC Pthreads-version)
Mac executable (PowerMac G5)
Mac executable (PowerMac G5 Pthreads-version)
RAxML-VI-HPC (version 2.2.3)and a comprehensive Manual (v2.2.3) RAxML-VI-HPC (version2.0.2) and a comprehensive Manual(v2.0)
RAxML-VI-HPC (version1.0) and a comprehensive Manual(v1.0)
RAxML-VI: Sequential program with significantly accelerated hill-climbing search algorithm for huge alignment data.
RAxML-III: Sequential program, includes more models of nucleotide substitution than RAxML-II.
RAxML-II: Sequential, Parallel, and Distributed implementation of RAxML with less model functionality.
Sequence and annotation data downloads are usually made available within the first week of the release of a new assembly. The download directories are automatically updated nightly to incorporate additions and modifications to the data.
You can download sequence and annotation data using our FTP server, but we recommend using rsync, which has the advantage of starting up where it left off after a failure, when run again. Please see the previous link for examples.
You can also download data from our Downloads page or our DAS server. To download a specific subset of the data or to configure the output format of the data, use the Table Browser. For information on extracting a large set of sequences from an assembly, seeExtracting sequence in batch from an assembly.
To quickly download large volumes of data you can use UDR (UDT Enabled Rysnc): UDR provides users much faster download rates. Here is an example using UDR, once installed, to downloadall the mouse mm9 ENCODE information that amounts to several terabytes:
A. Download the appropriate fasta files from our ftp server and extract sequence data using your own tools or the tools from our source tree. This is the recommended method when you have very large sequence datasets or will be extracting data frequently. Sequence data for most assemblies is located in the assembly's "chromosomes" subdirectory on the downloads server. For example,the sequence for human assembly hg17 can be found in You'll find instructions for obtaining our source programs and utilities here. Some programs that you may find useful are nibFrag and twoBitToFa, as well as other fa* programs. To obtain usage information about most programs, execute it without arguments.
The Genome Browser source code and executables are freely available for academic, nonprofit, and personal use (see Licensing the Genome Browser or Blat for commercial licensing requirements). The latest version of the source code may be downloaded here.
I downloaded the genome annotations from your MariaDB database tables, but the mRNA locations didn't match what was showing in the Genome Browser. Shouldn't they be in synch? Yes. The Genome Browser and Table Browser are both driven by the same underlying MariaDB database. Check that your downloaded tables are from the same assembly version as the one you are viewing in the Genome Browser. If the assembly dates don't match, the coordinates of the data within the tables may differ. In a very rare instance, you could also be affected by the brief lag time betweenthe update of the live databases underlying the Genome Browser and the time it takes for text dumps of these databases to become available in the downloads directory.
From the examples above, it can be seen that the strand to which an EST aligns is not necessarily reflected in the direction of transcription shown by the arrows in the display. When UCSC downloads mRNAs and ESTs from GenBank and aligns them to a genome assembly using Blat, each EST aligns to the + or - strand (forward or reverse direction) of the genome, which we record as + or - in the strand field of the corresponding database table, e.g. all_ests or chrN_est. The strand information (+/-) therefore indicates the direction of the match between the EST and the matching genomic sequence. Itbears no relationship to the direction of transcription of the RNA with which it might be associated. Determining the direction of transcription for ESTs is not an easy task so we do some calculations to make the best guess for the transcription direction.
It may have been added after we last downloaded data from GenBank, or it may have been replaced or removed. You can check the submission date and status of an accession on the NCBI Entrez Nucleotidesite.
If you wish to update a large number of coordinates to a different assembly and have access to a Linux platform, you may find it useful to try the command-line version of the LiftOver tool. The executable file for this utility can be downloaded here. LiftOver requires a pre-generated over.chain file as input, available for selected assemblies from the Downloads page. If the desired file is not available, send a request to the genome mailing list and we may be able to provide you with one.