MOTIVATION: Gene and species tree reconciliation methods are used to interpret gene trees, root them and correct uncertainties that are due to scarcity of signal in multiple sequence alignments. So far, reconciliation tools have not been integrated in standard phylogenetic software and they either lack performance on certain functions, or usability for biologists. RESULTS: We present Treerecs, a phylogenetic software based on duplication-loss reconciliation. Treerecs is simple to install and to use. It is fast and versatile, has a graphic output, and can be used along with methods for phylogenetic inference on multiple alignments like PLL and Seaview. AVAILABILITY AND IMPLEMENTATION: Treerecs is open-source. Its source code (C++, AGPLv3) and manuals are available from https://project.inria.fr/treerecs/.

BACKGROUND: Estimating the phylogenetic position of bacterial and archaeal organisms by genetic sequence comparisons is considered as the gold-standard in taxonomy. This is also a way to identify the species of origin of the sequence. The quality of the reference database used in such analyses is crucial: the database must reflect the up-to-date bacterial nomenclature and accurately indicate the species of origin of its sequences. DESCRIPTION: leBIBI(QBPP) is a web tool taking as input a series of nucleotide sequences belonging to one of a set of reference markers (e.g., SSU rRNA, rpoB, groEL2) and automatically retrieving closely related sequences, aligning them, and performing phylogenetic reconstruction using an approximate maximum likelihood approach. The system returns a set of quality parameters and, if possible, a suggested taxonomic assigment for the input sequences. The reference databases are extracted from GenBank and present four degrees of stringency, from the "superstringent" degree (one type strain per species) to the loosely parsed degree ("lax" database). A set of one hundred to more than a thousand sequences may be analyzed at a time. The speed of the process has been optimized through careful hardware selection and database design. CONCLUSION: leBIBI(QBPP) is a powerful tool helping biologists to position bacterial or archaeal sequence commonly used markers in a phylogeny. It is a diagnostic tool for clinical, industrial and environmental microbiology laboratory, as well as an exploratory tool for more specialized laboratories. Its main advantages, relatively to comparable systems are: i) the use of a broad set of databases covering diverse markers with various degrees of stringency; ii) the use of an approximate Maximum Likelihood approach for phylogenetic reconstruction; iii) a speed compatible with on-line usage; and iv) providing fully documented results to help the user in decision making.

BACKGROUND: To understand the evolutionary role of Lateral Gene Transfer (LGT), accurate methods are needed to identify transferred genes and infer their timing of acquisition. Phylogenetic methods are particularly promising for this purpose, but the reconciliation of a gene tree with a reference (species) tree is computationally hard. In addition, the application of these methods to real data raises the problem of sorting out real and artifactual phylogenetic conflict. RESULTS: We present Prunier, a new method for phylogenetic detection of LGT based on the search for a maximum statistical agreement forest (MSAF) between a gene tree and a reference tree. The program is flexible as it can use any definition of "agreement" among trees. We evaluate the performance of Prunier and two other programs (EEEP and RIATA-HGT) for their ability to detect transferred genes in realistic simulations where gene trees are reconstructed from sequences. Prunier proposes a single scenario that compares to the other methods in terms of sensitivity, but shows higher specificity. We show that LGT scenarios carry a strong signal about the position of the root of the species tree and could be used to identify the direction of evolutionary time on the species tree. We use Prunier on a biological dataset of 23 universal proteins and discuss their suitability for inferring the tree of life. CONCLUSIONS: The ability of Prunier to take into account branch support in the process of reconciliation allows a gain in complexity, in comparison to EEEP, and in accuracy in comparison to RIATA-HGT. Prunier's greedy algorithm proposes a single scenario of LGT for a gene family, but its quality always compares to the best solutions provided by the other algorithms. When the root position is uncertain in the species tree, Prunier is able to infer a scenario per root at a limited additional computational cost and can easily run on large datasets.Prunier is implemented in C++, using the Bio++ library and the phylogeny program Treefinder. It is available at: http://pbil.univ-lyon1.fr/software/prunier.

BACKGROUND: Comparative genomics is a central step in many sequence analysis studies, from gene annotation and the identification of new functional regions in genomes, to the study of evolutionary processes at the molecular level (speciation, single gene or whole genome duplications, etc.) and phylogenetics. In that context, databases providing users high quality homologous families and sequence alignments as well as phylogenetic trees based on state of the art algorithms are becoming indispensable. METHODS: We developed an automated procedure allowing massive all-against-all similarity searches, gene clustering, multiple alignments computation, and phylogenetic trees construction and reconciliation. The application of this procedure to a very large set of sequences is possible through parallel computing on a large computer cluster. RESULTS: Three databases were developed using this procedure: HOVERGEN, HOGENOM and HOMOLENS. These databases share the same architecture but differ in their content. HOVERGEN contains sequences from vertebrates, HOGENOM is mainly devoted to completely sequenced microbial organisms, and HOMOLENS is devoted to metazoan genomes from Ensembl. Access to the databases is provided through Web query forms, a general retrieval system and a client-server graphical interface. The later can be used to perform tree-pattern based searches allowing, among other uses, to retrieve sets of orthologous genes. The three databases, as well as the software required to build and query them, can be used or downloaded from the PBIL (Pôle Bioinformatique Lyonnais) site at http://pbil.univ-lyon1.fr/.

UNLABELLED: We present a web service allowing to automatically assign sequences to homologous gene families from a set of databases. After identification of the most similar gene family to the query sequence, this sequence is added to the whole alignment and the phylogenetic tree of the family is rebuilt. Thus, the phylogenetic position of the query sequence in its gene family can be easily identified. AVAILABILITY: http://pbil.univ-lyon1.fr/software/HoSeqI/.

Motivation: Comparative sequence analysis is widely used to study genome function and evolution. This approach first requires the identification of homologous genes and then the interpretation of their homology relationships (orthology or paralogy). To provide help in this complex task, we developed three databases of homologous genes containing sequences, multiple alignments and phylogenetic trees: HOBACGEN, HOVERGEN and HOGENOM. In this paper, we present two new tools for automating the search for orthologs or paralogs in these databases. Results: First, we have developed and implemented an algorithm to infer speciation and duplication events by comparison of gene and species trees (tree reconciliation). Second, we have developed a general method to search in our databases the gene families for which the tree topology matches a peculiar tree pattern. This algorithm of unordered tree pattern matching has been implemented in the FamFetch graphical interface. With the help of a graphical editor, the user can specify the topology of the tree pattern, and set constraints on its nodes and leaves. Then, this pattern is compared with all the phylogenetic trees of the database, to retrieve the families in which one or several occurrences of this pattern are found. By specifying ad hoc patterns, it is therefore possible to identify orthologs in our databases. Availability: The tree reconciliation program and the FamFetch interface are available from the Pôle Bioinformatique Lyonnais Web server at the following addresses: http://pbil.univ-lyon1.fr/software/RAP/RAP.htm and http://pbil.univ-lyon1.fr/software/famfetch.html Contact: [email protected]

SEAVIEW and PHYLO_WIN are two graphic tools for X Windows-Unix computers dedicated to sequence alignment and molecular phylogenetics. SEAVIEW is a sequence alignment editor allowing manual or automatic alignment through an interface with CLUSTALW program. Alignment of large sequences with extensive length differences is made easier by a dot-plot-based routine. The PHYLO_WIN program allows phylogenetic tree building according to most usual methods (neighbor joining with numerous distance estimates, maximum parsimony, maximum likelihood), and a bootstrap analysis with any of them. Reconstructed trees can be drawn, edited, printed, stored, evaluated according to numerous criteria. Taxonomic species groups and sets of conserved regions can be defined by mouse and stored into sequence files, thus avoiding multiple data files. Both tools are entirely mouse driven. On-line help makes them easy to use. They are freely available by anonymous ftp at biom3.univ-lyon1.fr/pub/ mol_phylogeny or http:@acnuc.univ-lyon1.fr/, or by e-mail to [email protected].

A method of interfacing sequence similarity search software with the fast sequence retrieval system ACNUC is described. The method is written in FORTRAN 77 and is straightforward to implement because no text-processing code is required--a minimum of 12 extra lines of FORTRAN provided the interface for most applications. The method is also efficient, since sequences are located by simple indexing techniques, with no linear searches of large database files necessary.

ACNUC is a database structure and retrieval software for use with either the GenBank or EMBL nucleic acid sequence data collections. The nucleotide and textual data furnished by both collections are each restructured into a database that allows sequence retrieval on a multi-criterion basis. The main selection criteria are: species (or higher order taxon), keyword, reference, journal, author, and organelle; all logical combinations of these criteria can be used. Direct access to sequence regions that code for a specific product (protein, tRNA or rRNA) is provided. A versatile extraction procedure copies selected sequences, or fragments of them, from the database to user files suitable to be analysed by user-supplied application programs. A detailed help mechanism is provided to aid the user at any time during the retrieval session. All software has been written in FORTRAN 77 which guarantees a high degree of transportability to minicomputers or mainframes. reference, journal, author, and organelle; all logical combinations of these criteria can be used. Direct access to sequence regions that code for a specific product (protein, tRNA or rRNA) is provided. A versatile extraction procedure copies selected sequences, or fragments of them, from the database to user files suitable to be analysed by user-supplied application programs. A detailed help mechanism is provided to aid the user at any time during the retrieval session. All software has been written in FORTRAN 77 which guarantees a high degree of transportability to minicomputers or mainframes.