Tools for de novo orthology prediction among genomes. What to choose?

More Panagiotis Provataris's questions See All

How do I correct for phylogenetic nonindependence between a binary/multistate categorical variable (independent) and a continuous depedent variable?

Dear community, I am rather new to phylogenetic comparative methods and seek your advice. I want to compare a continuous trait (dependent) between species belonging to either groupA and groupB...

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Can you fill a quick questionnaire?

Hi there, my name is Panagiotis Koilakos and I am studying computer science in AUEB, Greece. During an HCI(Human-Computer Interaction) course, we had to select a home device and try to beautify it...

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How can I remove false positives using the calculated bisulfite conversion rate in a WGBS experiment?

Dear community members, We have available WGBS data for a species. We used Bismark to map the reads to the reference genome. Unmethylated lambda phage DNA was spiked-in, to estimate the bisulfite...

18 July 2018 4,081 2 View

Is there a "stress test" for fish larvae which would reveal their stress resistance without implementing violent methods (i.e. lack of oxygen)?

I need to estimate the quality of fish larvae by estimating their stress resistance OR their resistance to the lack of oxygen. However due to ethical issues I need to use non-violent methods (i.e....

27 November 2017 1,824 3 View

Is there any questionnaire or survey conducted that have measured the satisfaction of companies from a Recruitment Process Outsourcing?

I'm trying to find a questionnaire that can measure the satisfaction rate of a company according the recruitment services that a Recruitment Agency provided.

18 November 2017 9,012 3 View

Hello I would like to ask you how we can add the different sulfur compounds in hysys for the crude distillation? Thank you!

Different forms of sulfur containing compounds.

04 July 2017 9,495 9 View

Can I remove taxa from pre-existing phylogeny before running a PGLS analysis?

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How can I know all the node coordinates where pressure is calculated as also the corresponding node ID using COMSOL?

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Is it possible to minimize an array of values (not just a simple function), using the genetic algorithm optimtool of Matlab?

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Safe concenctration of Guinidine hydrochloride in cell cultures?

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26 March 2016 3,983 4 View

IHC on mouse liver hepatocytes?

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Various schools have emerged in the study of comparative literature. Mention the most prominent of them in a nutshell.?

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Plasmid amplification in S2 cell?

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I am looking for a co-author specialised in decision-making/managerial studies/data science/?

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Statistical methods for comparing gene expression curves?

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Apart from MOFA what other software is available for analysis of a multi-omic study?

Study bringing together genomics, proteomics etc together

02 February 2021 2,856 2 View

How can i improve my DNA purity for whole genome sequence that has high 260/230 ratio ?

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Is there any alternative to BUSCO for searching orthologues within genomes available?

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Does someone know which structure could exit the olfactory bulbs at their antero-dorsal top ?

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27 January 2021 797 6 View

How to annotate list of gene names using Bash/R?

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Felipe Aguilera

Hi Panagiotis,

Orthofinder does exactly what you need. https://github.com/davidemms/OrthoFinder

Although it uses many additional software, it is super easier to use and gives you a list of orthologs genes in a 1:1 way. If you are planning to find orthologs genes among 50 species, I recommend you to use diamond for blast step instead of traditional blastp.

John Vollmers

Ican also recommend:

- proteinortho (Bidirectional Best Blast-hit based) : https://www.bioinf.uni-leipzig.de/Software/proteinortho/

-get_homologues (BDBH, COG-trianlges and/or OrthoMCL-based): https://github.com/eead-csic-compbio/get_homologues