Tag: MAFFT

Wu Z, McGoogan JM. Characteristics of and Important Lessons From the Coronavirus Disease 2019 (COVID-19) Outbreak in China: Summary of a Report of 72314 Cases From the Chinese Center for Disease Control and Prevention. JAMA. 2020;323(13):1239–42. Article  CAS  PubMed  Google Scholar  Kesheh MM, Hosseini P, Soltani S, Zandi M. An…

Damiani AM, de Vries M, Reimers G, Winkler S, Osterrieder N. A severe equine herpesvirus type 1 (EHV-1) abortion outbreak caused by a neuropathogenic strain at a breeding farm in northern Germany. Vet Microbiol. 2014;172(3–4):555–62. Article  PubMed  Google Scholar  Negussie H, Gizaw D, Tessema TS, Nauwynck HJ. Equine herpesvirus-1 myeloencephalopathy,…

Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410 CrossRef  CAS  PubMed  Google Scholar  Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database…

Van Valen, L. A new evolutionary law. Evol. Theory 1, 1–30 (1973). Google Scholar  Woolhouse, M. E. J., Webster, J. P., Domingo, E., Charlesworth, B. & Levin, B. R. Biological and biomedical implications of the co-evolution of pathogens and their hosts. Nat. Genet. 32, 569–577 (2002). Article  CAS  PubMed  Google…

Irish, S. R., Kyalo, D., Snow, R. W. & Coetzee, M. Updated list of Anopheles species (Diptera: Culicidae) by country in the Afrotropical Region and associated islands. Zootaxa 4747(3), 401–449. doi.org/10.1646/zootaxa.4747.3.1 (2020). Article  Google Scholar  Jacques, B. Les moustiques de l’archipel Comores. Série Entomologie Médicale et Parasitologie 15(2), 153–170 (1977)….

Knowles DP, Kappmeyer LS, Stiller D, Hennager SG, Perryman LE. Antibody to a recombinant merozoite protein epitope identifies horses infected with Babesia equi. J Clin Microbiol. 1992;30:3122–6. CAS  PubMed  PubMed Central  Google Scholar  Ueti MW, Palmer GH, Kappmeyer LS, Statdfield M, Scoles GA, Knowles DP. Ability of the vector tick…

Soltis, D. E. et al. Polyploidy and angiosperm diversification. Am. J. Bot. 96, 336–348 (2009). Article  PubMed  Google Scholar  Van de Peer, Y., Mizrachi, E. & Marchal, K. The evolutionary significance of polyploidy. Nat. Rev. Genet. 18, 411–424 (2017). Article  PubMed  Google Scholar  Amborella Genome Project et al. The Amborella…

Bacterial strains and growth conditions Veillonella parvula SKV38 was grown in SK medium (10 g/L tryptone [Difco], 10 g/L yeast extract [Difco], 0.4 g/L disodium phosphate, 2 g/L sodium chloride, and 10 ml/L 60% [wt/vol] sodium DL-lactate; described in ref. 51. Cultures were incubated at 37 °C in anaerobic conditions, either in anaerobic bags (GENbag anaero;…

Yabsley MJ, Shock BC. Natural history of zoonotic Babesia: role of wildlife reservoirs. Int J Parasitol Parasit Wildl. 2013;2:18–31. Article  Google Scholar  Hersh MH, Tibbetts M, Strauss M, Ostfeld RS, Keesing F. Reservoir competence of wildlife host species for Babesia microti. Emerg Infect Dis. 2012;18:1951–7. Article  PubMed  PubMed Central  Google…

Hebert, P. D. N., Cywinska, A., Ball, S. L. & deWaard, J. R. Biological identifications through DNA barcodes. Proc Biol Sci 270, 313–321 (2003). Article  CAS  PubMed  PubMed Central  Google Scholar  Huang, X., Ci, X., Conran, J. G. & Li, J. Application of DNA barcodes in Asian tropical trees –…

Egan, E. S., Fogel, M. A. & Waldor, M. K. Divided genomes: negotiating the cell cycle in prokaryotes with multiple chromosomes. Mol. Microbiol. 56, 1129–1138 (2005). Article  CAS  PubMed  Google Scholar  Harrison, P. W., Lower, R. P., Kim, N. K. & Young, J. P. Introducing the bacterial ‘chromid’: not a…

Sheridan, P. O. et al. Gene duplication drives genome expansion in a major lineage of Thaumarchaeota. Nat. Commun. 11, 1–12 (2020). Article  Google Scholar  Sheridan, P. O., Meng, Y., Williams, T. A. & Gubry-Rangin, C. Recovery of Lutacidiplasmatales archaeal order genomes suggests convergent evolution in Thermoplasmatota. Nat. Commun. 13, 1–13…

Chase, M. W. et al. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV. Bot. J. Linn. Soc. 181, 1–20 (2016). Article  Google Scholar  Jones, M. G. et al. Biosynthesis of the flavour precursors of onion and garlic. J. Exp. Bot….

Fich, E. A., Segerson, N. A. & Rose, J. K. C. The plant polyester cutin: biosynthesis, structure, and biological roles. Annu. Rev. Plant Biol. 67, 207–233 (2016). Article  CAS  PubMed  Google Scholar  Geldner, N. The endodermis. Annu. Rev. Plant Biol. 64, 531–558 (2013). Article  CAS  PubMed  Google Scholar  Calvo-Polanco, M….

This is easy because MAFFT is installed via Conda, but you have not activated that Conda environment, thus it will not give you access to the program. If you type … conda activate labinf mafft This will now work. To activate this inside a shell script you simply include the…

Animals for single-cell sequencing Adult samples of the aerial web-building spider (Hylyphantes graminicola) were collected from Anci district, Langfang, Hebei, China (39° 31.90’ N, 116° 38.15’ E) between September and October 2020. Collected spiders used for brain dissection were housed individually in a glass tube (Φ12 mm × 80 mm) at temperature- and humidity-controlled condition (24–26 °C and 50–60%…

Bacterial strains and phages Escherichia coli DH5a was routinely grown in Lysogeny broth (LB) medium and used for plasmid cloning, while E. coli BL21 (DE3) was used for protein production and the in vivo assays. E. coli phages T5, T7 and Lambda-vir are gifts from Shi Chen lab (Wuhan University,…

The Middle to Upper Palaeolithic transition in Europe is associated with the regional disappearance of Neanderthals and the spread of Homo sapiens. Archaeological evidence indicates the presence of technocomplexes at the interface of this transition, complicating our understanding of the period and the association of those with specific hominin groups….

Study design Experiments were performed in accordance with the New Zealand Animal Welfare Act (1999) and institutional guidelines provided by the University of Auckland Animal Ethics Committee, which reviewed and approved these experiments under application R1003. We did not use any specific randomisation process to allocate animals to a particular…

Hayes, E. B. Zika virus outside Africa. Emerg. Infect. Dis. 15(9), 1347–1350. doi.org/10.3201/eid1509.090442 (2009). Article  PubMed  PubMed Central  Google Scholar  Faye, O. et al. Molecular evolution of Zika virus during its emergence in the 20th century. PLoS Negl. Trop. Dis. 8(1), e2636. doi.org/10.1371/journal.pntd.0002636 (2014). Article  CAS  PubMed  PubMed Central  Google…

Introduction Antimicrobial resistance is a hidden global pandemic that shattered over 4.9 million people in 2019 alone, and the burden is highest, mainly in low-resource settings.1 Drug-resistant tuberculosis (DR-TB) caused by Mycobacterium tuberculosis (Mtb) complex (MTBC), which is resistant to one or more anti-TB drugs, is a leading global public…

Mushroom collecting Sporocarps were collected from various herbaria and during three expeditions to Point Reyes National Seashore (PRNS), California in 2004, 2014 and 2015, and in 2015 from three sites in Portugal. A total of 86 sporocarps were collected: 67 Californian sporocarps (one early herbarium sample dates to 1993), 11…

Bar-On YM, Phillips R, Milo R. The biomass distribution on Earth. Proc Natl Acad Sci USA. 2018;115:6506–11. Article  CAS  PubMed  PubMed Central  Google Scholar  Ogawa H, Amagai Y, Koike I, Kaiser K, Benner R. Production of refractory dissolved organic matter by bacteria. Science. 2001;292:917–20. Article  CAS  PubMed  Google Scholar  Liang…

Quesada A, Vincent WF. Strategies of adaptation by antarctic cyanobacteria to ultraviolet radiation. Eur J Phycol. 1997;32:335–42. Article  Google Scholar  Genuário DB, Corrêa DM, Komárek J, Fiore MF. Characterization of freshwater benthic biofilm-forming Hydrocoryne (Cyanobacteria) isolates from Antarctica. J Phycol. 2013;49:1142–53. Article  PubMed  Google Scholar  Makhalanyane TP, Valverde A, Gunnigle…

Learn how to install mafft on Debian 10 with this tutorial. mafft is Multiple alignment program for amino acid or nucleotide sequences Introduction In this tutorial we learn how to install mafft on Debian 10. What is mafft mafft is: MAFFT is a multiple sequence alignment program which offers three…

Protein sequence and prediction analysis The amino acid sequence of FcR was deduced from the F. cylindrus genome sequence33. Protein alignments with characterized microbial rhodopsins were performed using the MUSCLE algorithm implemented in Geneious (v.5.6)69. Predictions of subcellular location were performed with SignalP v.4.0 and TargetP (v.1.1)70. Putative transmembrane domains…

Name Last modified Size Description Parent Directory   –   align-clustalo.uwl 2019-09-24 01:05 3.0K   align-clustalw.uwl 2019-09-24 01:05 5.1K   align-kalign.uwl 2019-09-24 01:05 2.8K   align-mafft.uwl 2019-09-24 01:05 2.7K   align-tcoffee.uwl 2019-09-24 01:05 3.1K   align-to-reference.uwl 2019-09-24 01:05 3.1K   align.uwl 2019-09-24 01:05 2.7K   convert-msa.uwl 2019-09-24 01:05 1.4K  …

Genes coding for endo-chitinases (EC 3.2.1.14), the enzymes that cleave chitin polymers into oligomers [16], were found on 32 of 42 Endozoicomonadaceae genomes (Fig. 1 and Table S1), including representatives of all formally described genera and all Candidatus Gorgonimonas MAGs. Several genomes harbored more than one endo-chitinase encoding gene, resulting in…

World Health Organization. WHO Coronavirus (COVID-19) Dashboard. Available at covid19.who.int/ (2023). de Vries, M. et al. A comparative analysis of SARS-CoV-2 antivirals characterizes 3CLpro inhibitor PF-00835231 as a potential new treatment for COVID-19. J. Virol. 95, e01819-20 (2021). Article  PubMed  PubMed Central  Google Scholar  FDA. Emergency Use Authorization (Eua) of…

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Anderson, P. K. et al. Emerging infectious diseases of plants: Pathogen pollution, climate change and agrotechnology drivers. Trends Ecol. Evol. 19, 535–544. doi.org/10.1016/j.tree.2004.07.021 (2004). Article  PubMed  Google Scholar  Fisher, M. C. et al. Emerging fungal threats to animal, plant and ecosystem health. Nature 484, 186–194 (2012). Article  ADS  CAS  PubMed …

Taxon sampling and specimen collection All samples were collected legally following local requirements and our research complies with all relevant ethical regulations. Insect specimens were received at NC State University’s Insect Museum, pursuant to CITES permit 08US827653 (GRSCICOLL URI: grbio.org/cool/ij62-iybb). Our dataset contains representatives of 268 species from nine tribes,…

kulandai1 (Balamurugan) October 5, 2023, 9:21am 1 HiI am running qiime in hpc with pbs script, I got error as Traceback (most recent call last):File “/home/dell_emc/easybuild/software/QIIME2/2023.5/lib/python3.8/site-packages/q2cli/commands.py”, line 473, in callresults = action(**arguments)File “”, line 2, in align_to_tree_mafft_fasttreeFile “/home/dell_emc/easybuild/software/QIIME2/2023.5/lib/python3.8/site-packages/qiime2/sdk/action.py”, line 411, in parsl_wrappersetup_parallel()File “/home/dell_emc/easybuild/software/QIIME2/2023.5/lib/python3.8/site-packages/qiime2/sdk/parallel_config.py”, line 69, in setup_parallelconfig_fp = _get_vendored_config()File “/home/dell_emc/easybuild/software/QIIME2/2023.5/lib/python3.8/site-packages/qiime2/sdk/parallel_config.py”,…

Siguier, P., Gourbeyre, E., Varani, A., Ton-Hoang, B. & Chandler, M. Everyman’s guide to bacterial insertion sequences. Microbiol. Spectr. 3, MDNA3-0030-2014 (2015). Article  PubMed  Google Scholar  He, S. et al. The IS200/IS605 family and “peel and paste” single-strand transposition mechanism. Microbiol. Spectr. 3, MDNA3-0039-2014 (2015). Article  ADS  Google Scholar  Kapitonov,…

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Rubin, S., Parr, T., Da Costa, L. & Friston, K. Future climates: Markov blankets and active inference in the biosphere. J. R. Soc. Interface 17, 20200503 (2020). Article  CAS  PubMed  PubMed Central  Google Scholar  Cantonati, M. et al. Characteristics, main impacts, and stewardship of natural and artificial freshwater environments: Consequences…

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Yang, L. E. et al. Redefining Pyropia (Bangiales, Rhodophyta): Four new genera, resurrection of Porphyrella and description of Calidia pseudolobata sp. Nov. from China. J. Phycol. 56, 862–879 (2020). Article  CAS  PubMed  Google Scholar  Mumford Jr, T. F. Porphyra as Food: Cultivation and Economics in Algae and Human Affairs (ed….

In a recent article published in the journal Scientific Reports, researchers characterize five strains of gammacoronaviruses (gCoV) and deltacoronaviruses (dCoV) that were detected in black-headed gulls (Chroicocephalus ridibundus) and common gulls (Larus canus) in Poland. Study: Gulls as a host for both gamma and deltacoronaviruses. Image Credit: Nataliya Dorokhina / Shutterstock.com Background The Orthocoronavirinae subfamily consists…

Cultivations and harvest Cupriavidus necator strain DSMZ 428 was grown in Ralstonia Minimal Media (RMM) with 100 mM HEPES pH 7.5 under chemostat conditions in a Photon Systems Instruments Multi-Cultivator MC-1000 OD. Each reactor tube was set up to a volume of 55 mL, OD600 0.05 and 3.5 g/L fructose. Once growth ceased,…

Hi!I am facing a problem in alpha rarefaction curve plotting. In this study my samples were sequenced in two different runs “under same conditions” using Illumina Platform- MiSeq. For that reason I have merged the data from both the runs using same filtering parameters and following DADA2. Till “phylogeny align-to-tree-mafft-fasttree”…

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Isolation and microscopy of Mantamonas sphyraenae sp. nov Mantamonas sphyraenae SRT-306 was collected on 26 Sep. 2013 from the surface of a barracuda caught in a lagoon on Iriomote Island, Taketomi, Okinawa Prefecture, Japan (24° 23′ 36.762″ N, 123° 45′ 22.572″ E). It was isolated manually from the rough sample…

Mboowa G, Sserwadda I, Bulafu D, Chaplain D, Wewedru I, Seni J, et al. Transmission Dynamics of Antimicrobial Resistance at a National Referral Hospital in Uganda. Am J Trop Med Hyg. 2021;105(2):498–506. Article  CAS  PubMed  PubMed Central  Google Scholar  Rossolini GM, Arena F, Pecile P. Pollini SJCoip. Update on the…

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What programs allow you to find the mutation rate of many sequences without needing to calculate by hand? 0 Many methodologies require extensive calculation to determine mutation rate, but I am looking for a program (MAFFT, MEGA 11, BEAST, Arlequin, etc.) that has a feature that allows for the calculation…

Cryan JF, O’Riordan KJ, Cowan CSM, Sandhu KV, Bastiaanssen TFS, Boehme M, et al. The microbiota-gut-brain axis. Physiol Rev. 2019;99:1877–2013. Article  CAS  PubMed  Google Scholar  Lopetuso LR, Scaldaferri F, Petito V, Gasbarrini A. Commensal clostridia: leading players in the maintenance of gut homeostasis. Gut Pathog. 2013;5:e23. Article  Google Scholar  Collins…

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Dear all, We are excited to announce our upcoming online course on Phylogenomics, focused on Phylogenetic Inference and Divergence-Time Estimation with Genomic Data Sets. This course aims to provide researchers with the necessary tools and techniques to harness the power of genomic data for understanding evolutionary relationships and divergence times….

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Buettgens, M., Blavin, F. & Pan, C. The affordable care act reduced income inequality in the US. Health Aff. 40, 121–129 (2021). Article  Google Scholar  Chen, E. & Miller, G. E. Socioeconomic status and health: mediating and moderating factors. Annu. Rev. Clin. Psychol. 9, 723–749 (2013). Article  PubMed  Google Scholar …

Sample collection Previously, we collected nasal samples from WTD in northeastern Ohio focusing on metropolitan area parks11. In the present study, we expanded geographical study area by approximately 1000-fold to target the entire state of Ohio. We collected 1522 nasal swabs from WTD across 83 of Ohio’s 88 counties from…

Miterpáková M, Trbolová A, Hurníková Z, Balicka A, Čabanová V, Valentová D, et al. Thelazia callipaeda in Slovakia—from sporadic cases to endemic areas. Parasitol Int. 2022;87:102495. doi.org/10.1016/j.parint.2021.102495. Article  PubMed  Google Scholar  Gama A, Pires I, Canado M, Coutinho T, Lopes AP, Latrofa MS, et al. First report of Thelazia callipaeda…

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long PCR, 6000 bp, long indels (>100bp), multicopy gene = multiple amplicons from same PCR but only differ in indel meaning minimal substitutions: variance~1%, 2000 reads per sample, homopolymers (12bp) and tandem repeats (up to 55 fold, length 12-250bp), no reference available I want to de-noise my amplicons and generate…

Bond PL, Hugenholtz P, Keller J, Blackall LL. Bacterial community structures of phosphate-removing and non-phosphate-removing activated sludges from sequencing batch reactors. Appl Environ Microbiol. 1995;61:1910–6. Article  CAS  PubMed  PubMed Central  Google Scholar  Wang Z, Guo F, Liu L, Zhang T. Evidence of carbon fixation pathway in a bacterium from candidate…

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Introduction The worldwide spread of Klebsiella pneumoniae is a major global public health threat.1,2 K. pneumoniae is an opportunistic pathogen that colonizes the human gut and respiratory tract and possibly causes infection in immunocompromised hosts. Gut colonized K. pneumoniae is one of the important pathogens causing nosocomial infections, although the…

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Cowie RH. Annotated catalogue of species of Angiostrongylus and the related genera Gallegostrongylus, Rodentocaulus and Stefanskostrongylus (Nematoda: Metastrongyloidea, Angiostrongylidae). J Helminthol. 2019;93:389–423. Article  PubMed  Google Scholar  de Almeida LR, de Souza JGR, Santos HA, Torres EJL, Vilela R, do V, Cruz OMS, et al. Angiostrongylus minasensis n. sp.: new species…

Phylogenetic tree differ between including and excluding other species bacteria within same genus 0 Hello, I am new microbiology researcher currently researching bacteria using whole genome sequencing and currently doing analysis. I intend to create bacteria phylogenetic tree using BV-BRC services. The tree was succesfully created using MAFFT program with…

Baumgartner, K., Coetzee, M. P. A. & Hoffmeister, D. Secrets of the subterranean pathosystem of Armillaria: subterranean pathosystem of Armillaria. Mol. Plant Pathol. 12, 515–534 (2011). Article  PubMed  PubMed Central  Google Scholar  Heinzelmann, R. et al. Latest advances and future perspectives in Armillaria research. Can. J. Plant. Pathol. 41, 1–23…

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Multiple sequence aligment orientation 1 I’m seeking assistance with aligning multiple sequences using MAFFT. I’ve encountered a challenge as some of the sequences are on the forward strand, while others are on the reverse strand. I understand that for a successful multiple sequence alignment, all sequences need to have the…

A. I got this error (below) for this code physeq <- qza_to_phyloseq( features = “/Users/parikramasapkota/Desktop/CedricWind/durp_unpooled_rhizosphere/dada2_table_16S.qza”, tree = “/Users/parikramasapkota/Desktop/CedricWind/durp_unpooled_rhizosphere/phylogeny-align-to-tree-mafft-fasttree/rooted_tree.qza”, taxonomy = “/Users/parikramasapkota/Desktop/CedricWind/durp_unpooled_rhizosphere/taxonomy.qza”, metadata = “/Users/parikramasapkota/Desktop/CedricWind/durp_unpooled_rhizosphere/metadata16S.tsv” )Error in validObject(.Object) : invalid class “phyloseq” object:Component sample names do not match.Try sample_names() As I was trying to look into detail, this was the error,…

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Hello, I am experiencing the following error (below) when running the following command (below). I tried this command on multiple cloud instances with high specs, and I have tried running the artifact on the latest version of QIIME 2 after initially trying this on version QIIME2_2019.10. I even tried filtering…

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Subject: Need help with Qiime2 installation: ResolvePackageNotFound error Dear Qiime2 Community, I hope this message finds you well. I am currently facing an issue during the installation of Qiime2 and would greatly appreciate your assistance in resolving it. During the installation process, after following the Qiime2 instructions, I encountered the…

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Is it possible to get a pairwise distance matrix from a mafft alignment? 1 I’ve googled around a bit. From reading the publications and software documentation, its clear that there is a distance matrix being used but it doesnt seem possible to obtain. There is rumor of a –distout flag…

Patients Tumour tissues from seven HBsAg-positive patients (6 men, 1 woman; mean age 66.7 ± 8 years) with HBV-related HCC and paired adjacent non-tumour tissues from six of them were studied. The clinical, histological, and virologic characteristics of the patients are summarised in Table 1. Two normal liver samples from HBV-negative patients who…

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Sample collection Sampling kits were sent out to various bat rehabilitators in the UK, as described previously56, for the collection of faeces from bats. These faecal samples (0.02–1 g) were immediately stored in 5 ml of RNAlater solution to prevent degradation of RNA. The geographical locations and collection dates for all samples…

I did sequence alignment of a large peptide multi-fasta (n= 4991 sequences). The peptide alignment has sequences with the same length and pal2nal went through just fine… except some of the codon sequences are at half length. If average is X then some sequences are X/2. This is choking IQ-Tree….

Clinical RNA SARS-CoV-2 isolate For surveillance studies, a set of residual nasopharyngeal swab specimens positive for SARS-CoV-2 qRT-PCR from the Republican Diagnostic Centre (RDC) (umc.org.kz/en/) and private laboratory KDL “Olymp” (www.kdlolymp.kz/) were collected across the Republic of Kazakhstan between 2020 and 2022. 341 sequences that passed quality control are deposited…

Pal2nal translation of large multi-fasta files produces a codon translated file where some sequences half length of the average. 0 I did sequence alignment of a large peptide multi-fasta (n= 4991 sequences). The peptide alignment has sequences with the same length and pal2nal went through just fine… except some of…

The MAFFT algorithm is for gene level alignment of either protein or nucleotide sequences. If you want to align a large number of sequences in MegAlign Pro, we recommend using this algorithm. As of the Lasergene 17.3 release (August 2021), MegAlign Pro uses MAFFT7. This powerful aligner can typically align…

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Introduction Traditional Chinese herbal medicine plays an indispensable role in the treatment of multiple diseases in China and other developing countries (Newman et al., 2008). Apart from the traditional usage, many medicinal plants, such as Artemisia annua L. (artemisinin, Tu, 2016), Huperzia javanica (Sw.) C. Y. Yang (Huperzine A, Zangara, 2003;…

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Abstract Cotinus is an oligo‐specific ornamentally valuable genus with a disjunct distribution in the Northern Hemisphere. Traditionally, the taxonomy of Cotinus was mainly based on leaf morphological characteristics. However, the limited availability of genomic information greatly hindered the study of molecular evolution and phylogeny of this genus. This study sequenced…

Brief overview of inference approach Mutations occur during viral replication within infected individuals and these have the potential to be transmitted. During the epidemiological spread of an emerging virus or viral lineage, the virus population (distributed across infected individuals) thus accrues mutations and diversifies genetically. This joint process of viral…