Heidelberg Institute for Theoretical Studies

About: Heidelberg Institute for Theoretical Studies is a facility organization based out in Heidelberg, Germany. It is known for research contribution in the topics: Galaxy & Galaxy formation and evolution. The organization has 344 authors who have published 1293 publications receiving 94075 citations.

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies.

Abstract: Motivation: Phylogenies are increasingly used in all fields of medical and biological research. Moreover, because of the next-generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likelihood. Since the last RAxML paper in 2006, it has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community. Results: I present some of the most notable new features and extensions of RAxML, such as a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting postanalyses on sets of trees. In addition, an up-to-date 50-page user manual covering all new RAxML options is available. Availability and implementation: The code is available under GNU

VSEARCH: a versatile open source tool for metagenomics

Abstract: Background: VSEARCH is an open source and free of charge multithreaded 64-bit tool for processing and preparing metagenomics, genomics and population genomics nucleotide sequence data. It is designed as an alternative to the widely used USEARCH tool (Edgar, 2010) for which the source code is not publicly available, algorithm details are only rudimentarily described, and only a memory-confined 32-bit version is freely available for academic use. Methods: When searching nucleotide sequences, VSEARCH uses a fast heuristic based on words shared by the query and target sequences in order to quickly identify similar sequences, a similar strategy is probably used in USEARCH. VSEARCH then performs optimal global sequence alignment of the query against potential target sequences, using full dynamic programming instead of the seed-and-extend heuristic used by USEARCH. Pairwise alignments are computed in parallel using vectorisation and multiple threads. Results: VSEARCH includes most commands for analysing nucleotide sequences available in USEARCH version 7 and several of those available in USEARCH version 8, including searching (exact or based on global alignment), clustering by similarity (using length pre-sorting, abundance pre-sorting or a user-defined order), chimera detection (reference-based or de novo), dereplication (full length or prefix), pairwise alignment, reverse complementation, sorting, and subsampling. VSEARCH also includes commands for FASTQ file processing, i.e., format detection, filtering, read quality statistics, and merging of paired reads. Furthermore, VSEARCH extends functionality with several new commands and improvements, including shuffling, rereplication, masking of low-complexity sequences with the well-known DUST algorithm, a choice among different similarity definitions, and FASTQ file format conversion. VSEARCH is here shown to be more accurate than USEARCH when performing searching, clustering, chimera detection and subsampling, while on a par with USEARCH for paired-ends read merging. VSEARCH is slower than USEARCH when performing clustering and chimera detection, but significantly faster when performing paired-end reads merging and dereplication. VSEARCH is available at https://github.com/torognes/vsearch under either the BSD 2-clause license or the GNU General Public License version 3.0. Discussion: VSEARCH has been shown to be a fast, accurate and full-fledged alternative to USEARCH. A free and open-source versatile tool for sequence analysis is now available to the metagenomics community.

PEAR: a fast and accurate Illumina Paired-End reAd mergeR

Abstract: Motivation The Illumina paired-end sequencing technology can generate reads from both ends of target DNA fragments, which can subsequently be merged to increase the overall read length. There already exist tools for merging these paired-end reads when the target fragments are equally long. However, when fragment lengths vary and, in particular, when either the fragment size is shorter than a single-end read, or longer than twice the size of a single-end read, most state-of-the-art mergers fail to generate reliable results. Therefore, a robust tool is needed to merge paired-end reads that exhibit varying overlap lengths because of varying target fragment lengths. Results We present the PEAR software for merging raw Illumina paired-end reads from target fragments of varying length. The program evaluates all possible paired-end read overlaps and does not require the target fragment size as input. It also implements a statistical test for minimizing false-positive results. Tests on simulated and empirical data show that PEAR consistently generates highly accurate merged paired-end reads. A highly optimized implementation allows for merging millions of paired-end reads within a few minutes on a standard desktop computer. On multi-core architectures, the parallel version of PEAR shows linear speedups compared with the sequential version of PEAR. Availability and implementation PEAR is implemented in C and uses POSIX threads. It is freely available at http://www.exelixis-lab.org/web/software/pear.

Introducing the Illustris Project: simulating the coevolution of dark and visible matter in the Universe

Abstract: We introduce the Illustris Project, a series of large-scale hydrodynamical simulations of galaxy formation. The highest resolution simulation, Illustris-1, covers a volume of (106.5 Mpc)^3, has a dark mass resolution of 6.26 × 10^6 M_⊙, and an initial baryonic matter mass resolution of 1.26 × 10^6 M_⊙. At z = 0 gravitational forces are softened on scales of 710 pc, and the smallest hydrodynamical gas cells have an extent of 48 pc. We follow the dynamical evolution of 2 × 1820^3 resolution elements and in addition passively evolve 1820^3 Monte Carlo tracer particles reaching a total particle count of more than 18 billion. The galaxy formation model includes: primordial and metal-line cooling with self-shielding corrections, stellar evolution, stellar feedback, gas recycling, chemical enrichment, supermassive black hole growth, and feedback from active galactic nuclei. Here we describe the simulation suite, and contrast basic predictions of our model for the present-day galaxy population with observations of the local universe. At z = 0 our simulation volume contains about 40 000 well-resolved galaxies covering a diverse range of morphologies and colours including early-type, late-type and irregular galaxies. The simulation reproduces reasonably well the cosmic star formation rate density, the galaxy luminosity function, and baryon conversion efficiency at z = 0. It also qualitatively captures the impact of galaxy environment on the red fractions of galaxies. The internal velocity structure of selected well-resolved disc galaxies obeys the stellar and baryonic Tully–Fisher relation together with flat circular velocity curves. In the well-resolved regime, the simulation reproduces the observed mix of early-type and late-type galaxies. Our model predicts a halo mass dependent impact of baryonic effects on the halo mass function and the masses of haloes caused by feedback from supernova and active galactic nuclei.

Phylogenomics resolves the timing and pattern of insect evolution

Abstract: Insects are the most speciose group of animals, but the phylogenetic relationships of many major lineages remain unresolved. We inferred the phylogeny of insects from 1478 protein-coding genes. Phylogenomic analyses of nucleotide and amino acid sequences, with site-specific nucleotide or domain-specific amino acid substitution models, produced statistically robust and congruent results resolving previously controversial phylogenetic relations hips. We dated the origin of insects to the Early Ordovician [~479 million years ago (Ma)], of insect flight to the Early Devonian (~406 Ma), of major extant lineages to the Mississippian (~345 Ma), and the major diversification of holometabolous insects to the Early Cretaceous. Our phylogenomic study provides a comprehensive reliable scaffold for future comparative analyses of evolutionary innovations among insects.