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TreeDyn: towards dynamic graphics and annotations for analyses of trees
TLDR
TreeDyn is a tree visualization and annotation tool which includes tools for tree manipulation and annotation and uses meta-information through dynamic graphical operators or scripting to help analyses and annotations of single trees or tree collections.
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The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy
TLDR
The presence of both rRNA and rDNA sequences, taking into account introns (crucial for eukaryotic sequences), a normalized eight terms ranked-taxonomy and updates of new GenBank releases were made possible by a long-term collaboration between experts in taxonomy and computer scientists.
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Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water
TLDR
It is suggested that current understanding of the ecological complexity of protist communities, genetic diversity, and global species richness are severely limited by the sequence data hitherto available, and long‐tailed rank abundance curves suggest that the 454 sequencing approach provides improved access to rare genotypes.
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Marinobacter hydrocarbonoclasticus gen. nov., sp. nov., a new, extremely halotolerant, hydrocarbon-degrading marine bacterium.
TLDR
It is suggested that this bacterium isolated from Mediterranean seawater near a petroleum refinery be assigned to a new genus, at least temporarily, because of the impossibility of finding a single most closely related species.
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Phylogenetic relationships among marine Alteromonas-like proteobacteria: emended description of the family Alteromonadaceae and proposal of Pseudoalteromonadaceae fam. nov., Colwelliaceae fam. nov.,…
TLDR
The circumscription of the family Alteromonadaceae is limited to the genera Alteromonas and Glaciecola and the creation is proposed of the families Pseudoalteromondaceae fam.
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Phylogenetic analysis of the genera Alteromonas, Shewanella, and Moritella using genes coding for small-subunit rRNA sequences and division of the genus Alteromonas into two genera, Alteromonas…
TLDR
Small-subunit ribosomal DNA sequences were determined for 17 strains belonging to the genera Alteromonas, Shewanella, Vibrio, and Pseudomonas and these sequences were analyzed by phylogenetic methods, and it was suggested that the genus Alteromon as should be split into two genera.
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Midgut Microbiota of the Malaria Mosquito Vector Anopheles gambiae and Interactions with Plasmodium falciparum Infection
TLDR
Evidence is presented that the composition of the vector gut microbiota is one of the major components that determine the outcome of mosquito infections, and the abundance of Enterobacteriaceae in the mosquito midgut correlates significantly with the Plasmodium infection status.
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Elevation of three subspecies of Pectobacterium carotovorum to species level: Pectobacterium atrosepticum sp. nov., Pectobacterium betavasculorum sp. nov. and Pectobacterium wasabiae sp. nov.
TLDR
Biochemical criteria, deduced from a numerical taxonomy study of phenotypic characteristics and serological reactions, allowed discrimination of strains belonging to the four genomospecies and it is proposed to retain the P. carotovorum subspecies in the genus Pectobacterium.
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Patterns of Rare and Abundant Marine Microbial Eukaryotes
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Phylogenetic analysis and assessment of the genera Vibrio, Photobacterium, Aeromonas, and Plesiomonas deduced from small-subunit rRNA sequences.
TLDR
A phylogenetic analysis confirmed that the family Vibrionaceae should include only Photobacterium and Vibrio species; that Aeromonas species deserve family rank; and that Plesiomonas shigelloides is linked to the family Enterobacteriaceae.
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