Abstract：
BACKGROUND:The right sampling of homologous sequences for phylogenetic or molecular evolution analyses is a crucial step, the quality of which can have a significant impact on the final interpretation of the study. There is no single way for constructing datasets suitable for phylogenetic analysis, because this task intimately depends on the scientific question we want to address, Moreover, database mining softwares such as BLAST which are routinely used for searching homologous sequences are not specifically optimized for this task. RESULTS:To fill this gap, we designed BLAST-Explorer, an original and friendly web-based application that combines a BLAST search with a suite of tools that allows interactive, phylogenetic-oriented exploration of the BLAST results and flexible selection of homologous sequences among the BLAST hits. Once the selection of the BLAST hits is done using BLAST-Explorer, the corresponding sequence can be imported locally for external analysis or passed to the phylogenetic tree reconstruction pipelines available on the Phylogeny.fr platform. CONCLUSIONS:BLAST-Explorer provides a simple, intuitive and interactive graphical representation of the BLAST results and allows selection and retrieving of the BLAST hit sequences based a wide range of criterions. Although BLAST-Explorer primarily aims at helping the construction of sequence datasets for further phylogenetic study, it can also be used as a standard BLAST server with enriched output. BLAST-Explorer is available at http://www.phylogeny.fr.
journal_name
BMC Evol Bioljournal_title
BMC evolutionary biologyauthors
Dereeper A,Audic S,Claverie JM,Blanc Gdoi
10.1186/1471-2148-10-8subject
Has Abstractpub_date
2010-01-12 00:00:00pages
8issn
1471-2148pii
1471-2148-10-8journal_volume
10pub_type
杂志文章abstract：BACKGROUND:Probabilistic methods have progressively supplanted the Maximum Parsimony (MP) method for inferring phylogenetic trees. One of the major reasons for this shift was that MP is much more sensitive to the Long Branch Attraction (LBA) artefact than is Maximum Likelihood (ML). However, recent work by Kolaczkowski...
journal_title：BMC evolutionary biology
pub_type： 杂志文章
doi：10.1186/1471-2148-5-50
更新日期：2005-10-06 00:00:00
abstract：BACKGROUND:The tribe Lamprologini is the major substrate breeding lineage of Lake Tanganyika's cichlid species flock. Among several different life history strategies found in lamprologines, the adaptation to live and breed in empty gastropod shells is probably the most peculiar. Although shell-breeding arose several ti...
journal_title：BMC evolutionary biology
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doi：10.1186/1471-2148-7-7
更新日期：2007-01-25 00:00:00
abstract：BACKGROUND:Natural selection and genetic drift are major forces responsible for temporal genetic changes in populations. Furthermore, these evolutionary forces may interact with each other. Here we study the impact of an ongoing adaptive process at the molecular genetic level by analyzing the temporal genetic changes t...
journal_title：BMC evolutionary biology
pub_type： 杂志文章
doi：10.1186/1471-2148-8-66
更新日期：2008-02-26 00:00:00
abstract：BACKGROUND:There are around 400 internationally recognized dog breeds in the world today, with a remarkable diversity in size, shape, color and behavior. Breeds are considered to be uniform groups with similar physical characteristics, shaped by selection rooted in human preferences. This has led to a large genetic dif...
journal_title：BMC evolutionary biology
pub_type： 杂志文章
doi：10.1186/1471-2148-8-28
更新日期：2008-01-28 00:00:00
abstract：BACKGROUND:The genus Corbicula is one of the most invasive groups of molluscs. It includes both sexual and androgenetic lineages. The present study re-assessed the different morphotypes and haplotypes of West European Corbicula in order to clarify their taxonomic identification and phylogenetic relationships with Ameri...
journal_title：BMC evolutionary biology
pub_type： 杂志文章
doi：10.1186/1471-2148-11-147
更新日期：2011-05-27 00:00:00
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journal_title：BMC evolutionary biology
pub_type： 杂志文章
doi：10.1186/1471-2148-12-2
更新日期：2012-01-03 00:00:00
abstract：BACKGROUND:Unlike northern Europe and most of northern North America, the Eastern Palearctic and the northwesternmost tip of North America are believed to have been almost unglaciated during the Quarternary glacial periods. This could have facilitated long-term survival of many organisms in that area. To evaluate this,...
journal_title：BMC evolutionary biology
pub_type： 杂志文章
doi：10.1186/1471-2148-10-35
更新日期：2010-02-04 00:00:00
abstract：BACKGROUND:The classification of royal ferns (Osmundaceae) has long remained controversial. Recent molecular phylogenies indicate that Osmunda is paraphyletic and needs to be separated into Osmundastrum and Osmunda s.str. Here, however, we describe an exquisitely preserved Jurassic Osmunda rhizome (O. pulchella sp. nov...
journal_title：BMC evolutionary biology
pub_type： 杂志文章
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更新日期：2015-06-30 00:00:00
abstract：BACKGROUND:The blood-feeding behavior evolved multiple times in Insecta lineages and it represents an excellent opportunity to study patterns of convergent molecular evolution regarding this habit. In insects the expansion of some gene families is linked with blood-feeding behavior, but a wide study comparing the evolu...
journal_title：BMC evolutionary biology
pub_type： 杂志文章
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更新日期：2020-07-17 00:00:00
abstract：BACKGROUND:Prior to the sequencing of the human genome it was typically assumed that, tandem duplication aside, gene order is for the most part random. Numerous observers, however, highlighted instances in which a ligand was linked to one of its cognate receptors, with some authors suggesting that this may be a general...
journal_title：BMC evolutionary biology
pub_type： 杂志文章
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更新日期：2005-11-08 00:00:00
abstract：BACKGROUND:Selective pressure from pathogens is thought to shape the allelic diversity of major histocompatibility complex (MHC) genes in vertebrates. In particular, both local adaptation to pathogens and gene flow are thought to explain a large part of the intraspecific variation observed in MHC allelic diversity. To ...
journal_title：BMC evolutionary biology
pub_type： 杂志文章
doi：10.1186/s12862-017-0905-3
更新日期：2017-02-20 00:00:00
abstract：BACKGROUND:The currently recognized species richness of South American salamanders is surprisingly low compared to North and Central America. In part, this low richness may be due to the salamanders being a recent arrival to South America. Additionally, the number of South American salamander species may be underestima...
journal_title：BMC evolutionary biology
pub_type： 杂志文章
doi：10.1186/1471-2148-13-59
更新日期：2013-03-04 00:00:00
abstract：BACKGROUND:Genetic analyses of DNA sequences make use of an increasingly complex set of nucleotide substitution models to estimate the divergence between gene sequences. However, there is currently no way to assess the validity of nucleotide substitution models over short time-scales and with limited mutational accumul...
journal_title：BMC evolutionary biology
pub_type： 杂志文章
doi：10.1186/s12862-015-0312-6
更新日期：2015-03-11 00:00:00
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journal_title：BMC evolutionary biology
pub_type： 杂志文章
doi：10.1186/1471-2148-12-78
更新日期：2012-06-06 00:00:00
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journal_title：BMC evolutionary biology
pub_type： 杂志文章
doi：10.1186/1471-2148-11-223
更新日期：2011-07-28 00:00:00
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pub_type： 杂志文章
doi：10.1186/s12862-015-0335-z
更新日期：2015-03-31 00:00:00
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journal_title：BMC evolutionary biology
pub_type： 杂志文章
doi：10.1186/s12862-016-0850-6
更新日期：2017-01-03 00:00:00
abstract：BACKGROUND:Synonymous or silent mutations are usually thought to evolve neutrally. However, accumulating recent evidence has demonstrated that silent mutations may destabilize RNA structures or disrupt cis regulatory motifs superimposed on coding sequences. Such observations suggest the existence of stretches of codon ...
journal_title：BMC evolutionary biology
pub_type： 杂志文章
doi：10.1186/1471-2148-13-164
更新日期：2013-08-04 00:00:00
abstract：BACKGROUND:Sexual selection favours the evolution of male bioactive substances transferred during mating to enhance male reproductive success by affecting female physiology. These effects are mainly well documented for separate-sexed species. In simultaneous hermaphrodites, one of the most peculiar examples of transfer...
journal_title：BMC evolutionary biology
pub_type： 杂志文章
doi：10.1186/s12862-016-0672-6
更新日期：2016-05-13 00:00:00
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pub_type： 杂志文章
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更新日期：2020-10-19 00:00:00
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pub_type： 杂志文章
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更新日期：2016-09-09 00:00:00
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journal_title：BMC evolutionary biology
pub_type： 杂志文章
doi：10.1186/1471-2148-4-22
更新日期：2004-07-06 00:00:00
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journal_title：BMC evolutionary biology
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更新日期：2017-02-07 00:00:00
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journal_title：BMC evolutionary biology
pub_type： 杂志文章
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更新日期：2019-12-30 00:00:00
abstract：BACKGROUND:G protein-coupled receptors (GPCRs) constitute a large family of integral transmembrane receptor proteins that play a central role in signal transduction in eukaryotes. The genome of the protochordate Ciona intestinalis has a compact size with an ancestral complement of many diversified gene families of vert...
journal_title：BMC evolutionary biology
pub_type： 杂志文章
doi：10.1186/1471-2148-8-129
更新日期：2008-05-01 00:00:00
abstract：BACKGROUND:Morphological diversity among closely related animals can be the result of differing growth patterns. The Australian radiation of agamid lizards (Amphibolurinae) exhibits great ecological and morphological diversity, which they have achieved on a continent-wide scale, in a relatively short period of time (30...
journal_title：BMC evolutionary biology
pub_type： 杂志文章
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更新日期：2019-01-08 00:00:00
abstract：BACKGROUND:A central question for understanding the evolutionary responses of plant species to rapidly changing environments is the assessment of their potential for short-term (in one or a few generations) genetic change. In our study, we consider the case of Pinus pinaster Aiton (maritime pine), a widespread Mediterr...
journal_title：BMC evolutionary biology
pub_type： 杂志文章
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更新日期：2014-09-23 00:00:00
abstract：BACKGROUND:Chaetognaths, or arrow worms, are small marine, bilaterally symmetrical metazoans. The objective of this study was to analyse ribosomal protein (RP) coding sequences from a published collection of expressed sequence tags (ESTs) from a chaetognath (Spadella cephaloptera) and to use them in phylogenetic studie...
journal_title：BMC evolutionary biology
pub_type： 杂志文章
doi：10.1186/1471-2148-7-146
更新日期：2007-08-28 00:00:00
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journal_title：BMC evolutionary biology
pub_type： 杂志文章
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更新日期：2019-12-19 00:00:00
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journal_title：BMC evolutionary biology
pub_type： 杂志文章
doi：10.1186/s12862-016-0697-x
更新日期：2016-06-14 00:00:00
