Biomedical subjects

R Rozas

Publications and source records attributed to R Rozas.

5 recordsLinked to original sources

PubMed1999

DnaSP version 3: an integrated program for molecular population genetics and molecular evolution analysis.

UNLABELLED: DnaSP is a Windows integrated software package for the analysis of the DNA polymorphism from nucleotide sequence data. DnaSP version 3 incorporates several methods for estimating the amount and pattern of DNA polymorphism and divergence, and for conducting neutrality tests. AVAILABILITY: For academic uses, DnaSP is available free of charge from: http://www.bio.ub.es/julio/DnaSP.html CONTACT: julio@porthos.bio.ub.es

Computer Simulation↗

PubMed1997

DnaSP version 2.0: a novel software package for extensive molecular population genetics analysis.

MOTIVATION: Several methods in molecular population genetics have recently been described to estimate the amount and pattern of the DNA polymorphism in natural populations, and also to test the neutral theory of molecular evolution. These methods are essential for understanding the molecular evolutionary process. However, a comprehensive computer program for the analysis is not currently available. RESULTS: Here we present DnaSP (DNA Sequence Polymorphism) version 2.0, a software package for Windows that performs extensive population genetics analyses on DNA sequence data. DnaSP estimates several measures of DNA sequence variation within and between populations, linkage disequilibrium, recombination, gene flow and gene conversion (a new algorithm to detect gene conversion tracts has been included). DnaSP can also carry out several tests of neutrality: those of Fu and Li; Hudson, Kreitman and Aguadé; and Tajima. The results of the analyses are displayed in tabular and graphic form. AVAILABILITY: For academic uses, DnaSP is available via anonymous ftp: ftp.ebi.ac.uk in the directory/pub/software/dos.

Algorithms↗

PubMed1995

DnaSP, DNA sequence polymorphism: an interactive program for estimating population genetics parameters from DNA sequence data.

DnaSP, DNA sequence polymorphism, is an interactive computer program for the analysis of DNA polymorphism from nucleotide sequence data. The program, addressed to molecular population geneticists, calculates several measures of DNA sequence variation within and between populations, linkage disequilibrium parameters and Tajima's D statistic. The program, which is written in Visual Basic v. 3.0 and runs on an IBM-compatible PC under Windows, can handle a large number of sequences of up to thousands of nucleotides each.

Animals↗

PubMedDate not supplied

Exhaustive generation of organic isomers. 6. Stereoisomers having isolated and spiro cycles and new extended N_tuples.

A new stereoisomer generation system named CAMGEC2 for generation of stereoisomers containing isolated and spiro cycles with one or more descriptors among R, S, Z, E, M, and P is developed using Graph Theory. It includes new approaches for symmetry analysis, cycle detection processes in molecular graphs in a modular way, and also an extension of the N_tuple format for linear representation of molecular graphs that keeps graph topographical information.

Journal Article↗

PubMedDate not supplied

Algorithm for exhaustive and nonredundant organic stereoisomer generation.

Generation of organic stereoisomers with R/S, Z/E, and/or M/P configurations that may contain heteroatoms, multiple bonds, and any kind of cycle (isolated, spiro, condensed, and nested) is described. Inputs for processing are molecular structures in a N_tuple format resident on an automatic (canonical) or manual (non canonical) generated file which are processed by doing internal molecular graph construction, a weighted bipartite tree construction for all atoms and bonds to detect stereocenters, and symmetrical atom groups (SAG) with some specific SAG parameters that constitute a novel way for redundancy elimination of meso structures. Finally, determination of ligand CIP priorities allows for writing the output N_tuples with stereoisomer description. Several examples showing application of this methology to a wide number of structures are also presented.

Algorithms↗