Microarray Analysis
... Linz, by way of genomics data processing algorithms developed by the researchers and licensed by GNS.” ...
... Linz, by way of genomics data processing algorithms developed by the researchers and licensed by GNS.” ...
Typology now: Homology and developmental constraints explain
... the set of organisms’ morphological parts (the type) does change in phylogenetic lineages. The presence of a type (set of particular homologues) is due to the morphological-developmental make-up of organisms, and if the latter evolves in fundamental ways, the type can change. However, the present di ...
... the set of organisms’ morphological parts (the type) does change in phylogenetic lineages. The presence of a type (set of particular homologues) is due to the morphological-developmental make-up of organisms, and if the latter evolves in fundamental ways, the type can change. However, the present di ...
A Single Eubacterial Origin of Eukaryotic
... eight PFO sequences, including those from the anaerobic eukaryotes Entamoeba histolytica, Giardia lamblia, and Trichomonas vaginalis. They concluded that there was little support for a common ancestry of eukaryote PFO and that Entamoeba probably got its PFO independent of the other eukaryotes, and p ...
... eight PFO sequences, including those from the anaerobic eukaryotes Entamoeba histolytica, Giardia lamblia, and Trichomonas vaginalis. They concluded that there was little support for a common ancestry of eukaryote PFO and that Entamoeba probably got its PFO independent of the other eukaryotes, and p ...
phylogenetic tree
... ● There are three such trees with (2n-3)=5 leaves – they are distinct labelled branching patterns. ● There are then five ways of adding a further branch labelled with a distinct label (‘5’), giving in all 3x5=15 unrooted trees with five leaves. ● The number of unrooted trees with n leaves is equal ...
... ● There are three such trees with (2n-3)=5 leaves – they are distinct labelled branching patterns. ● There are then five ways of adding a further branch labelled with a distinct label (‘5’), giving in all 3x5=15 unrooted trees with five leaves. ● The number of unrooted trees with n leaves is equal ...
Seed plant phylogeny: Demise of the anthophyte
... angiosperms. Only a few analyses of ribosomal DNA linked angiosperms and Gnetales, and this with low statistical support. Analyses of the chloroplast gene rbcL placed Gnetales at the base of the seed plants, followed by angiosperms (an arrangement supported by more recent studies of photosystem gene ...
... angiosperms. Only a few analyses of ribosomal DNA linked angiosperms and Gnetales, and this with low statistical support. Analyses of the chloroplast gene rbcL placed Gnetales at the base of the seed plants, followed by angiosperms (an arrangement supported by more recent studies of photosystem gene ...
Random survival forests for highdimensional data
... different measures could yield different estimates of prediction error which ultimately could yield different selected variables. Equally importantly, there are scenarios where it may not even be clear how to measure prediction error. For example, in competing risks where the outcome is time Statist ...
... different measures could yield different estimates of prediction error which ultimately could yield different selected variables. Equally importantly, there are scenarios where it may not even be clear how to measure prediction error. For example, in competing risks where the outcome is time Statist ...
PPTX - Tandy Warnow
... • MetaPhyler, MetaPhlAn, and mOTU are marker-based techniques (but use different marker genes). ...
... • MetaPhyler, MetaPhlAn, and mOTU are marker-based techniques (but use different marker genes). ...
Sequence comparison of aflR from different Aspergillus species
... None None None None None Dorner et al. ...
... None None None None None Dorner et al. ...
View Tutorial
... the appearance of the first complete bacterial genome, Haemophilus influenzae, in 1995. Since then bacterial genomes have been sequenced at an exponential rate with a doubling time of about 20 months, and archaeal genomes have been sequenced with a doubling time of about 34 months [7]. With this rap ...
... the appearance of the first complete bacterial genome, Haemophilus influenzae, in 1995. Since then bacterial genomes have been sequenced at an exponential rate with a doubling time of about 20 months, and archaeal genomes have been sequenced with a doubling time of about 34 months [7]. With this rap ...
Title: Statistical Evidence for Common Ancestry
... under SA (see Materials and Methods). We also modified the tests to mask positions in which the exact same codon was used in all taxa, since such invariant codon usage at a position might be due to some unknown functional constraint (Figure 1, codon 2). In addition to testing the hypothesis that cod ...
... under SA (see Materials and Methods). We also modified the tests to mask positions in which the exact same codon was used in all taxa, since such invariant codon usage at a position might be due to some unknown functional constraint (Figure 1, codon 2). In addition to testing the hypothesis that cod ...
From Gene Trees with HGT to Species Trees
... A reconciliation map µ is TC if there is a gene-tree time map τT : V (T ) → R and species tree time map τT : V (T ) → R such that C0 u ≺T v =⇒ τT (u ) > τT (v ) C1 u ≺S v =⇒ τS (u ) > τS (v ) C2 If u speciation, then τT (u ) = τS (µ(u )) C3 If u is no speciation, then τS (x ) < τT (u ) < τS (y ) whe ...
... A reconciliation map µ is TC if there is a gene-tree time map τT : V (T ) → R and species tree time map τT : V (T ) → R such that C0 u ≺T v =⇒ τT (u ) > τT (v ) C1 u ≺S v =⇒ τS (u ) > τS (v ) C2 If u speciation, then τT (u ) = τS (µ(u )) C3 If u is no speciation, then τS (x ) < τT (u ) < τS (y ) whe ...
An rpoB signature sequence provides unique resolution for the
... NJ (Jukes–Cantor model) and MP trees were calculated by using MEGA4 (Tamura et al., 2007). ML trees were computed with Phyml v.2.4.1 (Guindon & Gascuel, 2003) and the HKY (Hasegawa– Kishino–Yano) model of nucleotide substitution (Hasegawa et al., 1985) using one category of substitution rate. For ea ...
... NJ (Jukes–Cantor model) and MP trees were calculated by using MEGA4 (Tamura et al., 2007). ML trees were computed with Phyml v.2.4.1 (Guindon & Gascuel, 2003) and the HKY (Hasegawa– Kishino–Yano) model of nucleotide substitution (Hasegawa et al., 1985) using one category of substitution rate. For ea ...
Giant viruses, giant chimeras: The multiple evolutionary histories of
... incorporated these genes from its eukaryotic host, the amoeba, into its own genome. While these studies were based on only a handful of genes, we sought here to understand how extensive was the role of HGT in shaping the whole Mimivirus genome, and which were the sources of the transferred genes. Th ...
... incorporated these genes from its eukaryotic host, the amoeba, into its own genome. While these studies were based on only a handful of genes, we sought here to understand how extensive was the role of HGT in shaping the whole Mimivirus genome, and which were the sources of the transferred genes. Th ...
canesbio
... • Cladistics groups organisms by common descent. • A clade is a group of species that includes an ancestral species and all its descendants. • Clades can be nested in larger clades, but not all groupings of organisms qualify as clades. ...
... • Cladistics groups organisms by common descent. • A clade is a group of species that includes an ancestral species and all its descendants. • Clades can be nested in larger clades, but not all groupings of organisms qualify as clades. ...
Bioinformatics - cs@union
... - Tree retained is one best meeting both optimality criteria and cooling schedule ...
... - Tree retained is one best meeting both optimality criteria and cooling schedule ...
Evolutionary history of the genus Capra
... The systematics of the genus Capra remain controversial in spite of studies conducted using morphology, mtDNA, and allozymes. Here, we assess the evolutionary history of Capra (i) using phylogenetic analysis of two nuclear genes located on the Y-chromosome and (ii) previously published and new cytoc ...
... The systematics of the genus Capra remain controversial in spite of studies conducted using morphology, mtDNA, and allozymes. Here, we assess the evolutionary history of Capra (i) using phylogenetic analysis of two nuclear genes located on the Y-chromosome and (ii) previously published and new cytoc ...
Learning Distance Functions in k-Nearest
... where wi is the weight for the i-th feature. Intuitively this can be understood as defining that one feature is more important than others when comparing two samples. The weights vector {w1 . . . wk } needs to be learned before classifying unknown samples. In their approach [12] the weights are lear ...
... where wi is the weight for the i-th feature. Intuitively this can be understood as defining that one feature is more important than others when comparing two samples. The weights vector {w1 . . . wk } needs to be learned before classifying unknown samples. In their approach [12] the weights are lear ...
Chapter 26 - Phylogeny and the Tree of Life
... Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings ...
... Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings ...
species
... • A molecular clock uses constant rates of evolution in some genes to estimate the absolute time of evolutionary change • In orthologous genes, nucleotide substitutions are proportional to the time since they last shared a common ancestor • In paralogous genes, nucleotide substitutions are proportio ...
... • A molecular clock uses constant rates of evolution in some genes to estimate the absolute time of evolutionary change • In orthologous genes, nucleotide substitutions are proportional to the time since they last shared a common ancestor • In paralogous genes, nucleotide substitutions are proportio ...
Cophylogeny and disparate rates of evolution in sympatric lineages
... (‘‘missing the boat’’; Paterson and Gray, 1997) may disrupt perfect correspondence among taxa. By comparing the phylogenies (or the data upon which those phylogenies are based) of hosts and their associates, it is possible to determine if statistically significant cophylogeny is present and discrimin ...
... (‘‘missing the boat’’; Paterson and Gray, 1997) may disrupt perfect correspondence among taxa. By comparing the phylogenies (or the data upon which those phylogenies are based) of hosts and their associates, it is possible to determine if statistically significant cophylogeny is present and discrimin ...
NOCARDIA sp. INDONESIAN VOLCANIC SOIL DESAK GEDE SRI ANDAYANI , ELIN YULINAH SUKANDAR
... using Clustal X and NJ plot program. To construct the phylogenetic trees, the homology sequence from BLAST and FASTA format results was calculated the data for three construction by Clustal X, and then conversion of calculated data into trees by NJ plot. Neighbors-joining (NJ) method is the simple p ...
... using Clustal X and NJ plot program. To construct the phylogenetic trees, the homology sequence from BLAST and FASTA format results was calculated the data for three construction by Clustal X, and then conversion of calculated data into trees by NJ plot. Neighbors-joining (NJ) method is the simple p ...
Module 8: Horizontal Gene Transfer
... 7. After clicking on the Image in PNG format (bitmap) in Figure 8.14 has been clicked, an unrooted phylogenetic tree similar to the one shown in Figure 8.15 will appear. A concise review of the interpretation of figure 8.14 can be found at: http://epidemic.bio.ed.ac.uk/how_to_read_a_phylogeny. A sum ...
... 7. After clicking on the Image in PNG format (bitmap) in Figure 8.14 has been clicked, an unrooted phylogenetic tree similar to the one shown in Figure 8.15 will appear. A concise review of the interpretation of figure 8.14 can be found at: http://epidemic.bio.ed.ac.uk/how_to_read_a_phylogeny. A sum ...
Introduction slides on BASE
... – How do I find interesting stuff? – learn some analysis tools – How do I trust the results? – statistics is key ...
... – How do I find interesting stuff? – learn some analysis tools – How do I trust the results? – statistics is key ...
Microarray Data Analysis Using BASE - MGH-PGA
... – How do I find interesting stuff? – learn some analysis tools – How do I trust the results? – statistics is key ...
... – How do I find interesting stuff? – learn some analysis tools – How do I trust the results? – statistics is key ...
Langfelder-NetworkDay-clustering
... A single setting works well and produces comparable results in many applications: Dynamic Tree Cut is suitable for automation ...
... A single setting works well and produces comparable results in many applications: Dynamic Tree Cut is suitable for automation ...