ALVIS 0.1 – Explorative Analysis and Visualisation of Multiple Sequence Alignments

ALVIS 0.1

:: DESCRIPTION

Alvis (Interactive non-aggregative multiple sequence ALignment VISualisation) is an open-source platform for the joint explorative analysis of MSAs and phylogenetic trees, employing Sequence Bundles as its main visualisation method.

::DEVELOPER

Goldman Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows /MacOsX
  • Java

:: DOWNLOAD

ALVIS

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2016 May 5;44(8):e77. doi: 10.1093/nar/gkw022.
ALVIS: interactive non-aggregative visualization and explorative analysis of multiple sequence alignments.
Schwarz RF, Tamuri AU, Kultys M, King J, Godwin J, Florescu AM, Schultz J, Goldman N.

PASSML / Passml_TM – Analysis of Phylogeny / Transmembrane Domain searching from Aligned Amino Acid Sequences

PASSML / Passml_TM

:: DESCRIPTION

PASSML (‘Phylogeny and Secondary Structure using Maximum Likelihood’) has been developed to implement an evolutionary model that combines protein secondary structure and amino acid replacement.

Passml_TM implement an evolutionary model that permits analysis of phylogeny and transmembrane domain searching from aligned amino acid sequences.

::DEVELOPER

Goldman Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 PASSML / Passml_TM

:: MORE INFORMATION

Citation

Bioinformatics. 1998;14(8):726-33.
PASSML: combining evolutionary inference and protein secondary structure prediction.
Liò P, Goldman N, Thorne JL, Jones3 DT.

rlsim 1.4 – Simulating RNA-seq library Preparation with Parameter Estimation

rlsim 1.4

:: DESCRIPTION

The rlsim package is a collection of tools for simulating RNA-seq library construction, aiming to reproduce the most important factors which are known to introduce significant biases in the currently used protocols: hexamer priming, PCR amplification and size selection.

::DEVELOPER

Goldman Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python
  • Biopython

:: DOWNLOAD

  rlsim

:: MORE INFORMATION

Citation:

Botond Sipos, Tim Massingham and Nick Goldman (2013):
rlsim – a package for simulating RNA-seq library preparation with parameter estimation.
http://bit.ly/rlsim-doc

SLR 1.4.3 – Sitewise Likehood Ratio Estimation of Selection

SLR 1.4.3

:: DESCRIPTION

SLR (Sitewise Likehood Ratio) is a program to detect sites in coding DNA that are unusually conserved and/or unusually variable (that is, evolving under purify or positive selection) by analysing the pattern of changes for an alignment of sequences on an evolutionary tree. The strength of selection at each site is determined by comparing the rate of nonsynonymous (amino acid changing) substitutions to that of synonymous (silent) substituions, the latter assumed to be invisible to selection and so evolving in a strictly neutral fashion.

::DEVELOPER

Goldman Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX

:: DOWNLOAD

 SLR

:: MORE INFORMATION

Citation:

Genetics. 2005 Mar;169(3):1753-62. Epub 2005 Jan 16.
Detecting amino acid sites under positive selection and purifying selection.
Massingham T, Goldman N.

AIS – Classify Amino Acids

AIS

:: DESCRIPTION

AIS (Almost Invariant Sets) is a program which uses a novel criterion and method to classify amino acids. The goal is to identify sets of amino acids with a high probability of change between elements of the set but small probability of change between different sets by using amino acid replacement matrices and their eigenvectors. After identification of the subsets the quality of the partition is assessed with a conductance measure

::DEVELOPER

Goldman Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 AIS

:: MORE INFORMATION

Citation:

Kosiol et al. (2004),
A new criterion and method for amino acid classification
Journal of Theoretical Biology 228:97-106.

EDIBLE 20110705 – Make Phylogenetic Information Calculations

EDIBLE 20110705

:: DESCRIPTION

EDIBLE (Experimental Design and Information By Likelihood Exploration.) is a software to perform likelihood calculations based on Markov process models of nucleotide substitution allied with phylogenetic trees, and from these to compute Fisher information measures under different experimental designs. These calculations can be used to answer questions of optimal experimental design in molecular phylogenetics.

::DEVELOPER

Goldman Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

 EDIBLE

:: MORE INFORMATION

Citation:

EDIBLE: experimental design and information calculations in phylogenetics.
Massingham T, Goldman N.
Bioinformatics. 2000 Mar;16(3):294-5.

Episomizer – Constuct Extrachromosomal Circular DNA using Whole Genome Sequencing Data

Episomizer

:: DESCRIPTION

Episomizer is currently a semi-automatic computational pipeline to construct circular DNA structures through identifying SVs connecting the boundaries of highly amplified CNA segments followed by a graph theoretical algorithm that searches for cyclic graphs.

::DEVELOPER

Zhang (Jinghui Zhang) Lab,St. Jude Children’s Research Hospital

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl
  • R
  • Python

:: DOWNLOAD

Episomizer

:: MORE INFORMATION

Citation

Xu K, Ding L, Chang TC, Chiang J, Mulder H, Wang S, Shaw TI, Wen J, Hover L, McLeod C, Wang YD, Easton J, Rusch M, Dalton J, Downing JR, Ellison DW, Zhang J, Baker SJ, Wu G.
Structure and evolution of double minutes in diagnosis and relapse brain tumors.
Acta Neuropathol. 2019 Jan;137(1):123-137. doi: 10.1007/s00401-018-1912-1.

RNAcode 0.3 – Analysis of Protein Coding Potential in Multiple Sequence Alignments

RNAcode 0.3

:: DESCRIPTION

RNAcode predicts protein coding regions in a a set of homologous nucleotide sequences. RNAcode relies on evolutionary signatures including synonymous/conservative mutations and conservation of the reading frame. It does not use any species specific sequence characteristics whatsoever and does not use any machine learning techniques.

::DEVELOPER

Goldman Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 RNAcode

:: MORE INFORMATION

Citation:

RNAcode: robust discrimination of coding and noncoding regions in comparative sequence data.
Washietl S, Findeiss S, Müller SA, Kalkhof S, von Bergen M, Hofacker IL, Stadler PF, Goldman N.
RNA. 2011;17(4):578-94.

RATS 1.0 – Resource Aware Taxon Selection

RATS 1.0

:: DESCRIPTION

RATS (Resource Aware Taxon Selection)

The phylogenetic diversity (PD) of a set of taxonomical units (e.g. genes, individuals, populations, species) is the total length of the evolutionary tree connecting them. This measure is relevant for choosing taxa in a variety of applications. In comparative genomics, the statistical power in testing various evolutionary hypotheses (e.g. low substitution rates) and in finding interesting genomic features (e.g. protein-coding genes, noncoding conserved elements) is strongly correlated with the total PD of the sequences being compared. Therefore, sequencing projects (both at the genome and gene level) should target taxa with a high total PD (see [1] and references therein). In biodiversity conservation, when not all species or populations in a geographical area can be protected, it is reasonable to concentrate conservation efforts on a subset with maximum PD [2].

Given the growing interest in PD, Fabio Pardi has worked on a hierarchy of optimisation problems where the aim is to select, from a collection of candidate taxa, a subset with maximum total PD. Depending on the nature of the constraints on this subset, the problems have varying computational complexity and different algorithmic solutions are devisable. When the aim is to select a fixed number of taxa, a simple greedy algorithm can be shown to produce optimal solutions [1]. When different taxa require different amounts of resources (money, time, etc.) for their selection (sequencing or conservation) and we have a limit on the total amount of resources available, however, it transpires that the problem is more difficult. We have devised a novel dynamic programming algorithm that can compute the optimal solution efficiently [3].

This algorithm is implemented by the program rats.

::DEVELOPER

Goldman Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  MacOsX

:: DOWNLOAD

 RATS

:: MORE INFORMATION

Citation:

Syst Biol. 2007 Jun;56(3):431-44.
Resource-aware taxon selection for maximizing phylogenetic diversity.
Pardi F, Goldman N.

cis-X v1.4.0 – Search for Activating Regulatory Variants in the Tumor Genome

cis-X v1.4.0

:: DESCRIPTION

cis-X is a new computational method for the discovery of noncoding regulatory variants in individual cancer genomes that will cause cis-activation of target gene transcription.

::DEVELOPER

Zhang (Jinghui Zhang) Lab,St. Jude Children’s Research Hospital

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

cis-X

:: MORE INFORMATION