From ppuigbo from urv.cat Wed May 9 10:18:26 2007 From: ppuigbo from urv.cat (ppuigbo@urv.cat) Date: Wed May 9 13:20:50 2007 Subject: [Bio-www] TOPD/FMTS: software to compare Phylogenetic trees Message-ID: I wish to introduce the TOPD/FMTS software to evaluate similarities and differences between phylogenetic trees. TOPD/FMTS can compare trees with leaf-sets that either completely or partially overlap and can be also used to compare two trees, one or both of which are multigene family trees. The version 1.0 of TOPD/FMTS implements the following methods to compare phylogenetic trees: - Split distance. - Nodal distance. - Disagree. - Taxa in common. - Quartets. - Triplets. Each option is also complemented with a randomisation analysis to test the null hypothesis that the similarity between two trees is not better than chance expectation. TOPD/FMTS is freely available at: http://genomes.urv.cat/topd . For more details see the article Puigbo et al. 2007. Bioinformatics doi: 10.1093/bioinformatics/btm135 . -------------------------------------------------------------------------------------------------------------------- Pere Puigb? Avalos, PhD Student Evolutionary Genomics Group, Biochemistry and Biotechnology Department, Rovira i Virgily University. C/Marcel?l? domingo s/n. 43007. Campus Sescelades. Tarragona. Phone: 0034.977.55.84.86 Web Page: http://genomes.urv.cat E-mail: ppuigbo@urv.cat -------------------------------------------------------------------------------------------------------------------- From ppuigbo from urv.cat Sun May 13 04:02:35 2007 From: ppuigbo from urv.cat (ppuigbo@urv.cat) Date: Sun May 13 08:06:11 2007 Subject: [Bio-www] OPTIMIZER: a web server for optimizing the codon usage of DNAsequences. Message-ID: I wish to introduce the OPTIMIZER web-server that optimizes the codon u= sage of a gene to increase its expression level=2E This web-server is fo= cused on the heterologous=2C or even homologous=2C gene expression in ba= cterial hosts=2E Two indices=2C CAI and ENc (effective number of codons)= =2C are used to measure the optimization process=2E Three methods of optimization are available=3A = - The =27one amino acid - one codon=27 method=2E - A guided random method based on a Monte Carlo algorithm=2E -The =91customized one amino acid - one codon=92 designed to max= imize the optimization with the fewest changes in the query sequence=2E = One of the main features of OPTIMIZER is that it makes it possible to o= ptimize a DNA sequence using the following pre-computed tables from more= than 150 prokaryotic species under strong translational selection=3A - Codon usage from a Predicted Group of Highly Expressed Genes=2E= - Codon usage from the Group of Ribosomal Protein Genes=2E - tRNA Gene Copy Numbers (tGCN)=2E Additionally=2C codon usage tables from the Codon Usage database (CUTG)= can also be used=2E OPTIMIZER is accessible free of charge at http=3A//genomes=2Eurv=2Ees/O= PTIMIZER =2E For more details see the article Puigbo et al=2E 2007 Nucleic Acids Rese= arch=2C doi=3A10=2E1093/nar/gkm219 =2E ------------------------------------------------------------------------= -------------------------------------------- Pere Puigb=F2 Avalos=2C PhD Student Evolutionary Genomics Group=2C Biochemistry and Biotechnology Department=2C Rovira i Virgily University=2E C/Marcel=B7l=ED domingo s/n=2E 43007=2E Campus Sescelades=2E Tarragona=2E= Phone=3A 0034=2E977=2E55=2E84=2E86 Web Page=3A http=3A//genomes=2Eurv=2Ecat E-mail=3A ppuigbo=40urv=2Ecat ------------------------------------------------------------------------= --------------------------------------------