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HOME
What we do. We are a research lab in the wonderful Ecology, Evolution, and Genetics department at the Australian National University in Canberra, Australia. We spend our time working on the genomes of a variety of organisms to understand how and why they change over time. Our work bridges spatial and temporal scales: from mutations thatoccur
PEOPLE - ROBERTLANFEAR.COM 2018 Group shot. Left to right: Minh, El, Caitlin, Raymond, Ashutosh, Rob, Suha, Bonnie (missing: Alejandro) Current lab members: Eleanor Beavan (PhD student)PUBLICATIONS
Lab members are shown in bold 2018 MinIONQC: fast and simple quality control for MinION sequencing data Lanfear R, Schalamun M, Kainer D, Wang W, Schwessinger B (2018) Bioinformatics bty654 PDF Do plants have a segregated germline?PARTITIONFINDER
PartitionFinder and PartitionFinderProtein are free open source programs for selecting best-fit partitioning schemes and models of molecular evolution for nucleotide and amino acid alignments. They take the hard work out of comparing partitioning schemes, and are useful in any situation where you want to compare or select partitioning schemes or models of molecular evolution. PARTITIONFINDER TUTORIAL PartitionFinder2 tutorial. This page provides a detailed step-by-step tutorial for comparing partitioning schemes for DNA sequence alignments using PartitionFinder2. TWO QUICK PLOTS TO VISUALISE GENDER BALANCE IN R In R, we start by loading a few libraries we’ll need later, and then reading in the data. library ( ggplot2) library ( reshape2) library ( plyr) all = read.csv ( "genderdata.csv") view raw gender.r hosted with by GitHub. Now we need to do a bit of work to set the order of the roles. The first couple of lines below would usually be sufficient CALCULATING AND INTERPRETING GENE- AND SITE-CONCORDANCE Tweet We (Minh Bui, Matt Hahn, and I) have just published a new version of IQ-TREE that calculates gene- and site-concordance factors for phylogenetic analyses. The application note describes the calculations, but doesn’t have much space for guidance on how to use and interpret the concordance factors. So that’s what this post is for. A gist with all the R code used for this post, as well PARTITIONFINDER2 MANUAL PartitionFinder2 = new methods for selecting partitioned models of evolution for phylogenetic analyses. 5 QuickStart – simple use cases In all of these examples, things in quotes and brackets (i.e. “”) indicate that you should use full file paths. PARTITIONFINDER: COMBINED SELECTION OF PARTITIONING PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses Robert Lanfear,*,1 Brett Calcott,1,2 Simon Y. W. Ho,3 and Stephane Guindon4 1Centre for Macroevolution and Macroecology, Ecology Evolution and Genetics, Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia COMPARING SHORT-READ MAPPERS FOR NON-MODEL SPECIES Both NextGenMap and BWA-MEM look good to mee. Both are quick (though NextGenMap is almost 3x quicker). Both map ~96% of the reads. BWA-MEM maps a few more good pairs, coverage looks about right for both, and most of the rest of the stats lookHOME
What we do. We are a research lab in the wonderful Ecology, Evolution, and Genetics department at the Australian National University in Canberra, Australia. We spend our time working on the genomes of a variety of organisms to understand how and why they change over time. Our work bridges spatial and temporal scales: from mutations thatoccur
PEOPLE - ROBERTLANFEAR.COM 2018 Group shot. Left to right: Minh, El, Caitlin, Raymond, Ashutosh, Rob, Suha, Bonnie (missing: Alejandro) Current lab members: Eleanor Beavan (PhD student)PUBLICATIONS
Lab members are shown in bold 2018 MinIONQC: fast and simple quality control for MinION sequencing data Lanfear R, Schalamun M, Kainer D, Wang W, Schwessinger B (2018) Bioinformatics bty654 PDF Do plants have a segregated germline?PARTITIONFINDER
PartitionFinder and PartitionFinderProtein are free open source programs for selecting best-fit partitioning schemes and models of molecular evolution for nucleotide and amino acid alignments. They take the hard work out of comparing partitioning schemes, and are useful in any situation where you want to compare or select partitioning schemes or models of molecular evolution. PARTITIONFINDER TUTORIAL PartitionFinder2 tutorial. This page provides a detailed step-by-step tutorial for comparing partitioning schemes for DNA sequence alignments using PartitionFinder2. TWO QUICK PLOTS TO VISUALISE GENDER BALANCE IN R In R, we start by loading a few libraries we’ll need later, and then reading in the data. library ( ggplot2) library ( reshape2) library ( plyr) all = read.csv ( "genderdata.csv") view raw gender.r hosted with by GitHub. Now we need to do a bit of work to set the order of the roles. The first couple of lines below would usually be sufficient CALCULATING AND INTERPRETING GENE- AND SITE-CONCORDANCE Tweet We (Minh Bui, Matt Hahn, and I) have just published a new version of IQ-TREE that calculates gene- and site-concordance factors for phylogenetic analyses. The application note describes the calculations, but doesn’t have much space for guidance on how to use and interpret the concordance factors. So that’s what this post is for. A gist with all the R code used for this post, as well PARTITIONFINDER2 MANUAL PartitionFinder2 = new methods for selecting partitioned models of evolution for phylogenetic analyses. 5 QuickStart – simple use cases In all of these examples, things in quotes and brackets (i.e. “”) indicate that you should use full file paths. PARTITIONFINDER: COMBINED SELECTION OF PARTITIONING PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses Robert Lanfear,*,1 Brett Calcott,1,2 Simon Y. W. Ho,3 and Stephane Guindon4 1Centre for Macroevolution and Macroecology, Ecology Evolution and Genetics, Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia COMPARING SHORT-READ MAPPERS FOR NON-MODEL SPECIES Both NextGenMap and BWA-MEM look good to mee. Both are quick (though NextGenMap is almost 3x quicker). Both map ~96% of the reads. BWA-MEM maps a few more good pairs, coverage looks about right for both, and most of the rest of the stats look RESEARCH - ROBERTLANFEAR.COM Research. Our work is motivated by the desire to understand molecular evolution, from the origin of mutations in individuals to their fixation in evolving lineages. To achieve this, we combine comparative methods, field work, genome sequencing, and evolutionary theory withPUBLICATIONS
Lab members are shown in bold 2018 MinIONQC: fast and simple quality control for MinION sequencing data Lanfear R, Schalamun M, Kainer D, Wang W, Schwessinger B (2018) Bioinformatics bty654 PDF Do plants have a segregated germline? JOIN - ROBERTLANFEAR.COM We're recruiting We have funding for domestic (Australian and NZ citizens) Honors and PhD students, and we're keen to support international applications for competitive scholarships too. PEOPLE - ROBERTLANFEAR.COM 2018 Group shot. Left to right: Minh, El, Caitlin, Raymond, Ashutosh, Rob, Suha, Bonnie (missing: Alejandro) Current lab members: Eleanor Beavan (PhD student) COMPARING SHORT-READ MAPPERS FOR NON-MODEL SPECIES Tweet Some background One of the first and most important steps in most genomics analyses is mapping your reads to a reference genome.If you work on a species without a reference genome, mapping can be particularly tricky - on top of errors from DNA extraction, library preps, and sequencing, you have the added headache that you might be expecting a lot of true biological PARTITIONFINDER FAQS In the .cfg file, set "search=user;" In the .cfg file, specify the partitioning scheme you want to use (see the manual for how to do this). Run PartitionFinder2 following the instructions in the manual. Your results will be printed out in the 'best_schemes.txt' file, which is in the /analysis folder. POPULATION SIZE AND THE RATE OF EVOLUTION Population size and the rate of evolution Robert Lanfear1,2, Hanna Kokko1, and Adam Eyre-Walker3 1Ecology 2 Evolution and Genetics, Research School of Biology, Australian National University, Canberra,ACT,
MITO-COMMUNICATIONS
MITO COMMUNICATION Mito-communications ROBERT LANFEAR1 & SIMON Y.W. HO2 1Centre for Macroevolution and Macroecology, Research School of Biology, Australian National University, Canberra, Australia, and 2School of Biological Sciences, University of Sydney, Sydney, Australia (Received 14 December 2011; accepted 27 December 2011) Mitochondrial mutation rates in the BACKUP PLANS FOR THE PARANOID ACADEMIC 3. Crashplan. This is also $10/month. It’s not as convenient as dropbox for day-to-day working, but it has unlimited storage. I use Crashplan to back up everything on I have on dropbox, as well as all of my raw data (currently ~50TB). (Note: these big raw data files are sequencing data, which are also held by the sequencing centre for awhile
PLANT MATING SYSTEMS OFTEN VARY WIDELY AMONG POPULATIONS Whitehead et al. Population Variation in Plant Mating Systems fewer than three population tm values with s.e. below or equal to this threshold. This quality control threshold wasHOME
Robert Lanfear's research, publications, and scripts. What we do We are a research lab in the wonderful Ecology, Evolution, and Genetics department at the Australian National University in Canberra, Australia. We spend our time working on the genomes of a variety of organisms to understand how and why they change over time. RESEARCH - ROBERTLANFEAR.COM Research. Our work is motivated by the desire to understand molecular evolution, from the origin of mutations in individuals to their fixation in evolving lineages. To achieve this, we combine comparative methods, field work, genome sequencing, and evolutionary theory with JOIN - ROBERTLANFEAR.COM We're recruiting We have funding for domestic (Australian and NZ citizens) Honors and PhD students, and we're keen to support international applications for competitive scholarships too.PUBLICATIONS
Lab members are shown in bold 2018 MinIONQC: fast and simple quality control for MinION sequencing data Lanfear R, Schalamun M, Kainer D, Wang W, Schwessinger B (2018) Bioinformatics bty654 PDF Do plants have a segregated germline?PARTITIONFINDER
PartitionFinder and PartitionFinderProtein are free open source programs for selecting best-fit partitioning schemes and models of molecular evolution for nucleotide and amino acid alignments. They take the hard work out of comparing partitioning schemes, and are useful in any situation where you want to compare or select partitioning schemes or models of molecular evolution. PARTITIONFINDER TUTORIAL PartitionFinder2 tutorial. This page provides a detailed step-by-step tutorial for comparing partitioning schemes for DNA sequence alignments using PartitionFinder2. TWO QUICK PLOTS TO VISUALISE GENDER BALANCE IN R In R, we start by loading a few libraries we’ll need later, and then reading in the data. library ( ggplot2) library ( reshape2) library ( plyr) all = read.csv ( "genderdata.csv") view raw gender.r hosted with by GitHub. Now we need to do a bit of work to set the order of the roles. The first couple of lines below would usually be sufficient PARTITIONFINDER2 MANUAL PartitionFinder2 = new methods for selecting partitioned models of evolution for phylogenetic analyses. 5 QuickStart – simple use cases In all of these examples, things in quotes and brackets (i.e. “”) indicate that you should use full file paths. PARTITIONFINDER: COMBINED SELECTION OF PARTITIONING PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses Robert Lanfear,*,1 Brett Calcott,1,2 Simon Y. W. Ho,3 and Stephane Guindon4 1Centre for Macroevolution and Macroecology, Ecology Evolution and Genetics, Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia COMPARING SHORT-READ MAPPERS FOR NON-MODEL SPECIES Both NextGenMap and BWA-MEM look good to mee. Both are quick (though NextGenMap is almost 3x quicker). Both map ~96% of the reads. BWA-MEM maps a few more good pairs, coverage looks about right for both, and most of the rest of the stats lookHOME
Robert Lanfear's research, publications, and scripts. What we do We are a research lab in the wonderful Ecology, Evolution, and Genetics department at the Australian National University in Canberra, Australia. We spend our time working on the genomes of a variety of organisms to understand how and why they change over time. RESEARCH - ROBERTLANFEAR.COM Research. Our work is motivated by the desire to understand molecular evolution, from the origin of mutations in individuals to their fixation in evolving lineages. To achieve this, we combine comparative methods, field work, genome sequencing, and evolutionary theory with JOIN - ROBERTLANFEAR.COM We're recruiting We have funding for domestic (Australian and NZ citizens) Honors and PhD students, and we're keen to support international applications for competitive scholarships too.PUBLICATIONS
Lab members are shown in bold 2018 MinIONQC: fast and simple quality control for MinION sequencing data Lanfear R, Schalamun M, Kainer D, Wang W, Schwessinger B (2018) Bioinformatics bty654 PDF Do plants have a segregated germline?PARTITIONFINDER
PartitionFinder and PartitionFinderProtein are free open source programs for selecting best-fit partitioning schemes and models of molecular evolution for nucleotide and amino acid alignments. They take the hard work out of comparing partitioning schemes, and are useful in any situation where you want to compare or select partitioning schemes or models of molecular evolution. PARTITIONFINDER TUTORIAL PartitionFinder2 tutorial. This page provides a detailed step-by-step tutorial for comparing partitioning schemes for DNA sequence alignments using PartitionFinder2. TWO QUICK PLOTS TO VISUALISE GENDER BALANCE IN R In R, we start by loading a few libraries we’ll need later, and then reading in the data. library ( ggplot2) library ( reshape2) library ( plyr) all = read.csv ( "genderdata.csv") view raw gender.r hosted with by GitHub. Now we need to do a bit of work to set the order of the roles. The first couple of lines below would usually be sufficient PARTITIONFINDER2 MANUAL PartitionFinder2 = new methods for selecting partitioned models of evolution for phylogenetic analyses. 5 QuickStart – simple use cases In all of these examples, things in quotes and brackets (i.e. “”) indicate that you should use full file paths. PARTITIONFINDER: COMBINED SELECTION OF PARTITIONING PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses Robert Lanfear,*,1 Brett Calcott,1,2 Simon Y. W. Ho,3 and Stephane Guindon4 1Centre for Macroevolution and Macroecology, Ecology Evolution and Genetics, Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia COMPARING SHORT-READ MAPPERS FOR NON-MODEL SPECIES Both NextGenMap and BWA-MEM look good to mee. Both are quick (though NextGenMap is almost 3x quicker). Both map ~96% of the reads. BWA-MEM maps a few more good pairs, coverage looks about right for both, and most of the rest of the stats look RESEARCH - ROBERTLANFEAR.COM Research. Our work is motivated by the desire to understand molecular evolution, from the origin of mutations in individuals to their fixation in evolving lineages. To achieve this, we combine comparative methods, field work, genome sequencing, and evolutionary theory with JOIN - ROBERTLANFEAR.COM We're recruiting We have funding for domestic (Australian and NZ citizens) Honors and PhD students, and we're keen to support international applications for competitive scholarships too. PEOPLE - ROBERTLANFEAR.COM 2018 Group shot. Left to right: Minh, El, Caitlin, Raymond, Ashutosh, Rob, Suha, Bonnie (missing: Alejandro) Current lab members: Eleanor Beavan (PhD student)PUBLICATIONS
Lab members are shown in bold 2018 MinIONQC: fast and simple quality control for MinION sequencing data Lanfear R, Schalamun M, Kainer D, Wang W, Schwessinger B (2018) Bioinformatics bty654 PDF Do plants have a segregated germline? CONTACT - ROBERT LANFEAR Email rob.lanfear@anu.edu.au Phone +61 2 6125 2536 Mail Room 207, Building 116 Daley Road, Australian National University, Canberra, ACT2601 Australia
COMPARING SHORT-READ MAPPERS FOR NON-MODEL SPECIES Tweet Some background One of the first and most important steps in most genomics analyses is mapping your reads to a reference genome.If you work on a species without a reference genome, mapping can be particularly tricky - on top of errors from DNA extraction, library preps, and sequencing, you have the added headache that you might be expecting a lot of true biological BACKUP PLANS FOR THE PARANOID ACADEMIC 3. Crashplan. This is also $10/month. It’s not as convenient as dropbox for day-to-day working, but it has unlimited storage. I use Crashplan to back up everything on I have on dropbox, as well as all of my raw data (currently ~50TB). (Note: these big raw data files are sequencing data, which are also held by the sequencing centre for awhile
POPULATION SIZE AND THE RATE OF EVOLUTION Population size and the rate of evolution Robert Lanfear1,2, Hanna Kokko1, and Adam Eyre-Walker3 1Ecology 2 Evolution and Genetics, Research School of Biology, Australian National University, Canberra,ACT,
PLANT MATING SYSTEMS OFTEN VARY WIDELY AMONG POPULATIONS Whitehead et al. Population Variation in Plant Mating Systems fewer than three population tm values with s.e. below or equal to this threshold. This quality control threshold was MOL. BIOL. EVOL. KEY WORDS partitioning scheme with the best fit to the data (Schwarz 1978; Burnham and Anderson 2002). For any given partitioning scheme, an appropriate model of molecular evolution needs to be chosen for each group of sites before a phylogenetic analysis can be performed. THE LANFEAR LAB @ANU MOLECULAR EVOLUTION AND PHYLOGENETICSMenu
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WHAT WE DO
We are a research lab in the wonderful Ecology, Evolution, andGenetics department
at the Australian National University in Canberra, Australia. We spend our time working on the genomes of a variety of organisms to understand how and why they change over time. Our work bridges spatial and temporal scales: from mutations that occur within a single individual over a few decades, to the long-term evolution of globally-distributed clades of species over millions of years. We also work on theoretical aspects of molecular evolution, and develop new statistical methods and software to analyse huge DNA datasets. Behind all of this is a drive to understand some of biology's big questions, from the existence and functions of germlines to attempts to infer the tree of all life. The best way to get a good idea of what we do is to take a look at our publications.JOIN US!
If you're interested in joining us, please get in touch , we'd love to hear from you. You don't need lots of experience, just enthusiasm and a willingness to apply yourself. We can accommodate undergrads, Honors students, PhD Students, and PostDocs. We are interested in folks with diverse backgrounds and welcome new project ideas and collaborations.CONTACT
rob.lanfear@anu.edu.au+61 2 6125 2536
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