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GUIDANCE Server - a web server for assessing alignment confidence scoreGUIDANCE: a web server for assessing alignment confidence score
http://guidance.tau.ac.il/
GUIDANCE: a web server for assessing alignment confidence score
http://guidance.tau.ac.il/
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GUIDANCE Server - a web server for assessing alignment confidence score | guidance.tau.ac.il Reviews
https://guidance.tau.ac.il
GUIDANCE: a web server for assessing alignment confidence score
GUIDANCE Server - a web server for assessing alignment confidence score
http://guidance.tau.ac.il/ver2/overview.php
Server for alignment confidence score. What is GUIDANCE good for? What is GUIDANCE not good for? Number of bootstrap repeats. Advanced MAFFT PRANK options. What are the GUIDANCE scores? Constructing the set of MSAs. Calculation of the GUIDANCE scores. What are the HoT scores? MSA Colored according to the confidence score. Remove unreliable columns below a certain cutoff. Remove unreliable sequences below a certain cutoff. Mask specific residues below a certain cutoff. Multiple sequence alignment (MSA) is...
GUIDANCE Server - a web server for assessing alignment confidence score
http://guidance.tau.ac.il/ver2/credits.php
Server for alignment confidence score. GUIDANCE2 citing and credits. When citing the GUIDANCE2 server please refer to:. Sela, I., Ashkenazy, H., Katoh, K. and Pupko, T. (2015). GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters. Nucleic Acids Research, 2015 Jul 1; 43 (Web Server issue): W7-W14. Doi: 10.1093/nar/gkq443 [ABS]. Landan, G., and D. Graur. (2008). Local reliability measures from sets of co-optimal multiple sequence alignments.
GUIDANCE Server - a web server for assessing alignment confidence score
http://guidance.tau.ac.il/ver2/source.php
Server for alignment confidence score. 1 Downloading and compiling GUIDANCE. Downloading and Compiling GUIDANCE. The following instructions should work right out of the box for UNIX-like systems. Mac should also work in principle, but is not yet supported. Windows will require some additional work, such as setting up a cygwin environment. 1 Download the GUIDANCE source code. 2015, November 24 - releasing version 2.01:. 2014, September 7 - releasing version 2.0:. 2014, August 7 - releasing version 1.5:.
GUIDANCE Server - a web server for assessing alignment confidence score
http://guidance.tau.ac.il/ver2/Gallery.php
Server for alignment confidence score. To view an example output page for an alignment of Vpu proteins. Color coding scheme of GUIDANCE. Note that if those sequences are removed, the trans-membrane domain will become a confidently aligned block (Figure 1b). Subsequent analyses based on this MSA should take the alignment uncertainty into account. For example, if our goal is positive selection inference (see the Selecton server.
GUIDANCE Gallery
http://guidance.tau.ac.il/ver2/Gallery/output.php
GUIDANCE2 Job Status - FINISHED. GUIDANCE is now processing your request. This page will be automatically updated every 30 seconds. You can also reload it manually. Once the job has finished, several links to the output files will appear below. If you wish to view these results at a later time without recalculating them, please bookmark this page. The results will be kept in the server for three months. Sequences = vpu.fas. Advanced Alignment Parameters: - reorder. Generating the base alignment. 0049 (98...
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PICS-Ord: unlimited coding of ambiguous regions by pairwise identity and cost scores ordination - De Rerum Natura
http://dererumnatura.us/archives/2011/01/pics-ord-unlimi.html
PICS-Ord: unlimited coding of ambiguous regions by pairwise identity and cost scores ordination. By Reed A. Cartwright. January 25, 2011 8:37 PM. I’ve had the good fortune of having some papers published recently. The first one is a methodology paper concerning a way of extracting phylogenetic information from regions of multiple sequence alignments that are full of indels and difficult to align:. PICS-Ord: unlimited coding of ambiguous regions by pairwise identity and cost scores ordination. That provid...
Software - Privman lab: evolutionary genomics of social insects
http://privman.haifa.ac.il/index.php/software
Privman lab: evolutionary genomics of social insects. Estimation of confidence scores for individual alignment positions or individual residues, and filtering or masking of these unreliable positions to reduce errors in downstream analyses such as positive selection inference (dN/dS methods). A searchable collection of homing endonucleases and their predicted target sequences for gene targeting applications. Vailable as part of the. Developed by Igor Chebotar.
Methods - Selectome
http://selectome.unil.ch/cgi-bin/methods.cgi
Selectome: a Database of Positive Selection. CodeML is a program from the package PAML. It estimates various parameters (Ts/Tv, dN/dS, branch length) on the codon (nucleotide) alignment, according to the phylogenetic tree. The parameter of interest to us is ω = dN/dS. Which indicates selective pressure. Selectome uses the branch-site model. Which estimates different dN/dS values among branches and among sites. A branch of interest is selected and called ". 34; All other branches in the tree are the ".
Publications - Privman lab: evolutionary genomics of social insects
http://privman.haifa.ac.il/index.php/publications
Privman lab: evolutionary genomics of social insects. Google Scholar author page. Goncalves AN, Menin L, Ortiz D, Riba-Grognuz O, Koto A, Soares ZG, Privman E, Miska EA, Benton R, Keller L. 2016. Oral transfer of chemical cues, growth proteins and hormones in social insects. 12 Lucas ER, Privman E, Keller L. 2016. Higher expression of somatic repair genes in long-lived ant queens than workers. Proc R Soc B. 9 Simola DF, Wissler L, Donahue G, Waterhouse RM,. 5 Barzel A*,. Peeri M, Naor A, Shachar E, Burst...
Alignments
http://www.molbiol-tools.ca/Alignments.htm
GENESTREAM SEARCH network server IGH Montpellier, France). Finds multiple matching subsegments in two sequences. Provides one with % identity for different subsegments of the sequence. Jaroszewski, L. et al. 2011. Nucleic Acids Res. 39. Compare Two Sequences with LALIGN/PLALIGN. Local Alignments - offers the user a graphic dotplot output of the alignments. Compares a protein sequence to a genomic DNA sequence, allowing for introns and frameshifting errors. Alignment tool for protein (ExPASy, Switzerland).
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GUIDANCE Server - a web server for assessing alignment confidence score
Server for alignment confidence score. GUIDANCE is not suitable for alignments of very few sequences. As a rule of thumb, use GUIDANCE2 or HoT for less than 8 sequences. Upload your sequences file (FASTA format only). Select the MSA algorithm. PRANK is significantly more time consuming. MAFFT is the fastest. Select the MSA algorithm. PRANK is significantly more time consuming. MAFFT is the fastest. Please enter your email address (Optional). Enter a descriptive job title for your GUIDANCE query.
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