Tag: Nexus

mrbayes checkpoint file not starting from linux or windows after accidental closing

mrbayes checkpoint file not starting from linux or windows after accidental closing 0 Division 1 has 284 unique site patterns Initializing conditional likelihoods Using standard non-SSE likelihood calculator for division 1 (single-precision) Getting values from previous run Executing file “C:\Users\Public\Documents\ngfrphylogeny3\mrbayesfasta1209c.nex.ckp” UNIX line termination Longest line length = 60503 Parsing file…

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Maternal diet induces persistent DNA methylation changes in the muscle of beef calves

Gicquel, C., El-Osta, A. & Le Bouc, Y. Epigenetic regulation and fetal programming. Best Pract. Res. Clin. Endocrinol. Metab. 22, 1–16 (2008). CAS  Google Scholar  Godfrey, K. M. & Barker, D. J. Fetal programming and adult health. Public Health Nutr. 4, 611–624 (2001). CAS  Google Scholar  Encinias, H. B., Lardy,…

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maven – Best practice sharing a Openapi yaml between Backend and Frontend

in my new project we are using Openapi to share the API endpoints with each other. At the moment the yaml is part of the backend project and we copy it the frontend to create the client interface with the openapi generator. No the plan is to push the yaml…

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Difference between python and biopython

Biopython vs Python Hi, Please help – If already have python 3 in laptop, is biopython still needed to download? I already downloaded python 3; when I checked on the www.bippython.org, there is also “download”, are they the same or different? sorry if it is a naive question. Thank you…

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logits to softmax pytorch

A tag already exists with the provided branch name. Join the PyTorch developer community to contribute, learn, and get your questions answered. Space – falling faster than light? We are converting the layers using ReLu and other neural networks. Learn more, including about available controls: Cookies Policy. In addition, the…

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Scientists pinpoint druggable target in aggressive breast cancer — ScienceDaily

Researchers at VCU Massey Cancer Center have set their sights on a new therapeutic target for an aggressive form of breast cancer with limited treatment options. Breast cancer is the second most common cancer in U.S. women, and triple-negative breast cancer (TNBC) is a more aggressive and deadly form of…

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Long non-coding RNA SNHG6 couples cholesterol sensing with mTORC1 activation in hepatocellular carcinoma

Chu, B. B. et al. Cholesterol transport through lysosome-peroxisome membrane contacts. Cell 161, 291–306 (2015). CAS  Article  Google Scholar  Luo, J., Yang, H. & Song, B. L. Mechanisms and regulation of cholesterol homeostasis. Nat. Rev. Mol. Cell Biol. 21, 225–245 (2020). CAS  Article  Google Scholar  Luo, J., Jiang, L., Yang,…

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Lecturer/Senior Lecturer in Bioinformatics and Computational Biology | University of New South Wales

Job Details Salary Lecturer – Level B, $111,563 to $131,517 per annum + 17% superannuation Senior Lecturer – Level C, $135,504 to $155,460 per annum + 17% superannuation Full time 5-year Convertible Tenure Track (CTT) Location: Kensington – Sydney, Australia The Opportunity Join the School of Computer Science and Engineering…

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Integrative analysis of eQTL and GWAS summary statistics reveals transcriptomic alteration in Alzheimer brains | BMC Medical Genomics

Significant gene-AD associations With the GWAS summary data from the IGAP and eQTL summary data from BRAINEAC, we performed both SMR and HEIDI tests to estimate the gene-AD associations in three human brain regions: frontal cortex, temporal cortex, and hippocampal regions. For the frontal cortex and hippocampal regions, we obtained…

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phylogenetics – Biopython reads my tree eternally long

I have a nexus tree (1332 taxa) with a lot of additional data. When I tried to read it through tree = Phylo.read(treepath, “nexus”), my kernel got eternally loaded. If I abort the process, I get the following message: ————————————————————————— KeyboardInterrupt Traceback (most recent call last) Input In [95], in…

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Postdoctoral Scientist – Knott Lab

Details Posted: 09-Apr-22 Location: Los Angeles, California Type: Full-time Salary: Open Categories: Staff/Administrative Internal Number: HRC0544032D Principal Investigator, Simon Knott, PhD is looking for a Postdoctoral Scientist to join the team! The Cedars-Sinai Center for Bioinformatics and Functional Genomics (CBFG) is an integrated, interdisciplinary research group with the common goal…

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Pollinator sharing, copollination, and speciation by host shifting among six closely related dioecious fig species

Sampling Six dioecious fig species (F. erecta, F. formosana, F. vaccinioides, F. abelii, F. pyriformis, and F. variolosa) and their pollinator wasp species were examined in this study. As mentioned in the Introduction, these fig species were considered to be well suited for this study because they are distributed in…

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H2O is an in-memory platform for distributed, scalable machine learning

H2O is an in-memory platform for distributed, scalable machine learning. H2O uses familiar interfaces like R, Python, Scala, Java, JSON and the Flow notebook/web interface, and works seamlessly with big data technologies like Hadoop and Spark. H2O provides implementations of many popular algorithms such as Generalized Linear Models (GLM), Gradient…

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Fasta file reading python

Answer by Aidan Golden I think you can just use Biopython,It is indeed wrong today. I edited the answer since it has been possible to use str(sequence) for a long time now.,Very useful answer from 7 years ago! FYI, in current version of biopython(1.69), fasta.seq.tostring() is obsolete, use str(fasta.seq) instead.,Nicely…

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Postdoctoral Scientist – Knott Lab – Bioinformatics & Functional Genomics

Requisition # HRC0544032C Principal Investigator, Simon Knott, PhD is looking for a Postdoctoral Scientist to join the team! The Cedars-Sinai Center for Bioinformatics and Functional Genomics (CBFG) is an integrated, interdisciplinary research group with the common goal of developing end-to-end research workflows for genomic and high-throughput functional analysis of patient…

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Handy online tool for genomic analysis and data visualization

Previously, I have recommended two powered online tools for genomic analysis and data visualization here. I want to share with you other handy tools that I found recently. iTOL is perfect for beautifying genomic data. circos is useful for displaying the relationships between objects and positions. You could discover their…

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Postdoctoral Scientist – Knott Lab – Bioinformatics & Functional Genomics – Los Angeles

**Principal Investigator, Simon Knott, PhD is looking for a Postdoctoral Scientist to join the team!** The Cedars-Sinai Center for Bioinformatics and Functional Genomics (CBFG) is an integrated, interdisciplinary research group with the common goal of developing end-to-end research workflows for genomic and high-throughput functional analysis of patient samples. The primary…

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Remove non variable sites from sequence alignment

Remove non variable sites from sequence alignment 0 I’m looking for suggestions for programs that will remove nonvariable sites from a fasta/phylip/nexus alignment. I have very large sequence alignments, and I am hoping only to retain variable sites. MSA alignment nexus FASTA sequence • 12 views Login before adding your…

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