RAxML Workbench is a JAVA-based Graphical User Interface package for running and analyzing short read placement runs with the RAxML EPA algorithm.
This stand-alone GUI is similar in functionality to the EPA web-server. It also allows you to build reference trees with RAxML for the original full-length sequence alignment.
Get RAxML Workbench and give it a go to fully assess its capabilities!

 

Download ✯✯✯ DOWNLOAD (Mirror #1)

Download ✯✯✯ DOWNLOAD (Mirror #1)

 

 

 

 

 

RAxML Workbench Free PC/Windows

(RAxML v8.0.6)

JAVA Version: 1.8

Supported Platform: Windows

Supported Browser: IE8+, Chrome, Firefox

Web Site:

JAVA Windows Binary:

Unzip the Zip file to local directory.

Untar the Zip and copy the raxml.bat, raxml.jar, and raxml.properties files to the RAxML Workbench Crack For Windows application folder. For example, the current installation location is: C:\raraxml

Double-click raxml.bat and follow the instructions, which will perform setup.

Double-click raxml.jar and follow the instructions.

Double-click raxml.properties and follow the instructions.

Activate the raxml.properties file.

Check the appropriate box and input your RAxML EPA log location in raxml.properties. The default location for raxml.properties and raxml.bat is C:\raraxml\EPA

Double-click raxml.jar to start RAxML Workbench.

RAxML Workbench should launch and open the stand-alone EPA application.

Select Build a Reference Tree from the Right-Click menu and follow the instructions. If you use the standalone EPA application the instructions will be slightly different.

NOTE:

There are two different raxml.jar files. raxml.jar is a JAR file that contains some of the RaxML source code and support libraries. raxml.jar is only needed if you want to build a reference tree for your project with RAxML.

raxml.bat is a batch file that launches the full RaxML EPA algorithm. raxml.bat is only needed if you have installed RAxML and do not wish to run the EPA algorithm on a tree built with the standalone EPA application.

The following is the simple procedure to follow while running RAxML Workbench, assuming that you have installed RAxML and have build a full-length alignment of your Newick formatted reference tree:

Create Newick formatted sequences for your reference tree and select the best model fit for your data.

Select

RAxML Workbench Download PC/Windows (Latest)

Newick output is used by default for RAxML
TreeView from JAX-Tree is used for display
Tree view supports hierarchical display
The majority of annotating functionality can be done through custom mouse clicks
It is most similar to TreeView from JAX-Tree or JTree
Protein Sequences can be added as nodes
Taxa can be added as nodes
Tips and Comments (including branch lengths) can be added to nodes
Mappings and alignments can be created through Custom actions
When run in batch mode, a line per tree is produced and one annotation per line
Timing for each node is shown
ALN, PG, BP, and ML are calculated, and annotated if requested

Other general features:

Open dialog can be used to add sequence names, tip names, comments, and branch lengths to the tree
The same kind of tree can be edited multiple times
Edits are made in the tree, but do not change the underlying sequences
Edits are stored in the sequence names, comments, tip names, branch lengths, and other annotations
Edits can be removed by selecting edit, and then removing a node from the list
A node can be copied and moved to a new node
There are options to save and load the tree, and revert the last saved tree

Known Issues:

The alignments tab is not currently working. We are working on fixing this.

Projects to keep in touch with:

EvoNexus project to post all of the MSA files so you don’t have to download them
ALB project to be able to add in your own custom alignments
AlbEvoNexus (Alignment-Based Evolutionary Network, to be a complementary addition to our ALB project)

Chambers (

Presentation on EVOEXPRESS

Presentation at BioExpo Europe

Showcase on the EVOEXPRESS website

Testimonial (from user Pielman):

«It’s been a pleasure to use the EPA on the bipartitioning example I posted on the project. Based on my results, the EPA will definitely be part of the next release of EvoMap!»

AP is a lightweight, extensible software environment
aa67ecbc25

RAxML Workbench With Serial Key Free

Manage reference alignments and their NJ and MP tree models, and analyze short read placement runs
with the RAxML error correction and rate heterogeneity estimation and rejection algorithm.
The EPA (Explicit Phylogenetic Analysis) approach is comprised of a tree building algorithm that is capable of fast, accurate phylogenetic inference from short sequence reads, and an associated model of rate heterogeneity. The EPA model assumes that all branches have a similar rate of evolution, but that branch lengths are not known. Rather than specifying separate branch lengths directly, the EPA model is estimated by inputting branch lengths from a separate reference phylogeny.
RAxML Workbench feature highlights:
Run and analyze short read placements with the RAxML EPA algorithm
Generate NJ and MP trees from alignments
Create reference alignments for the original full-length sequence alignment
View and edit branch lengths in reference tree model
Get and edit detailed statistics on EPA run performance.
Highlight informative nodes in reference tree
Display and plot branch lengths and informative variable sites
EPA root placement estimation and SNP discovery
Display informative nodes in reference tree:
The EPA algorithm estimates the root position as the common node in the reference alignment of which the smallest number of branch lengths are missing. This node is generally the node with the fewest number of informative sites, i.e. variable sites, and variable sites are also more likely to be correct. Often the root position is identical to the root node in the reference tree.
To choose the root position, you may first wish to infer a root node position by setting the option «Infer Root from Aligned» to «no.» This will result in the root node of the reference tree being used as the root of the NJ or MP tree. Note that the root node position is inferred with the highest likelihood to be correct. Alternatively, you may also choose to estimate the root node position from an existing reference tree.
Display and plot informative variable sites:
The EPA algorithm finds informative sites by identifying variable sites in the reference tree and estimating branch lengths to the variable sites. The most likely root node of the reference tree is taken as the root node of the NJ or MP tree. This can be useful in situations where you want to know if the root node of the reference tree is identical to the root node of the NJ or MP tree.
EPA runs analysis on:
Alignments with the fast stand-alone version of RAxML
FastTree XML file with the stand-alone RAxML

What’s New In?

RaxML Workbench is a JAVA-based Graphical User Interface package for running and analyzing short read placement runs with the RAxML EPA algorithm.
This stand-alone GUI is similar in functionality to the EPA web-server. It also allows you to build reference trees with RAxML for the original full-length sequence alignment.
Get RAxML Workbench and give it a go to fully assess its capabilities!

This package has been downloaded 10727 times via sourceforge since June, 2007.

Last updated on Sun, 03 Mar 2014 07:18:18 GMT

Next release (3.2) will be ready about a week after April Fools’ Day, 2013.

This package has been downloaded 10727 times via sourceforge since June, 2007.

Last updated on Sun, 03 Mar 2014 07:19:20 GMT

Previous release (2.7) was on Oct 30, 2012.

This package has been downloaded 22335 times via sourceforge since June, 2007.

Last updated on Sun, 03 Mar 2014 07:19:42 GMT

Next release (2.8) will be ready about a week after November 5, 2012.

This package has been downloaded 11798 times via sourceforge since June, 2007.

Last updated on Sun, 03 Mar 2014 07:19:42 GMT

Previous release (2.7) was on Oct 30, 2012.

This package has been downloaded 11798 times via sourceforge since June, 2007.

Last updated on Sun, 03 Mar 2014 07:19:21 GMT

Next release (2.7) will be ready about a week after August 17, 2012.

This package has been downloaded 11798 times via sourceforge since June, 2007.

Last updated on Sun, 03 Mar 2014 07:19:16 GMT

Previous release (2.6) was on Jul 26, 2012.

This package has been downloaded 11778 times via sourceforge since June, 2007.

Last updated on Sun, 03 Mar 2014 07:19:35 GMT

Next release (2.6) will be ready about a week after August 17, 2012.

This package has been downloaded 11778 times via sourceforge since June, 2007.

Last updated on Sun, 03 Mar 2014 07:19:31 GMT

Previous release (2.5) was on Feb 14, 2012

System Requirements For RAxML Workbench:

Internet Explorer 9.0 or later is required to download an update to the game. The game can also be played in Internet Explorer 8, 8.5, and 9.
Download or update Internet Explorer 9.0 or later. Internet Explorer 9.0 or later is required to download an update to the game. The game can also be played in Internet Explorer 8, 8.5, and 9.
Minimum System Requirements:
Microsoft Windows XP/Vista/7/8/10/X64 (64-bit) is required

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