Pan-European study of genotypes and phenotypes in the Arabidopsis relative Cardamine hirsuta reveals how adaptation, demography, and development shape diversity patterns.

We study natural DNA polymorphisms and associated phenotypes in the Arabidopsis relative Cardamine hirsuta. We observed strong genetic differentiation among several ancestry groups and broader distribution of Iberian relict strains in European C. hirsuta compared to Arabidopsis. We found synchronization between vegetative and reproductive development and a pervasive role for heterochronic pathways in shaping C. hirsuta natural variation. A single, fast-cycling ChFRIGIDA allele evolved adaptively allowing range expansion from glacial refugia, unlike Arabidopsis where multiple FRIGIDA haplotypes were involved. The Azores islands, where Arabidopsis is scarce, are a hotspot for C. hirsuta diversity. We identified a quantitative trait locus (QTL) in the heterochronic SPL9 transcription factor as a determinant of an Azorean morphotype. This QTL shows evidence for positive selection, and its distribution mirrors a climate gradient that broadly shaped the Azorean flora. Overall, we establish a framework to explore how the interplay of adaptation, demography, and development shaped diversity patterns of 2 related plant species.

Genome-wide scans for selective sweeps using convolutional neural networks.

MOTIVATION: Recent methods for selective sweep detection cast the problem as a classification task and use summary statistics as features to capture region characteristics that are indicative of a selective sweep, thereby being sensitive to confounding factors. Furthermore, they are not designed to perform whole-genome scans or to estimate the extent of the genomic region that was affected by positive selection; both are required for identifying candidate genes and the time and strength of selection. RESULTS: We present ASDEC (https://github.com/pephco/ASDEC), a neural-network-based framework that can scan whole genomes for selective sweeps. ASDEC achieves similar classification performance to other convolutional neural network-based classifiers that rely on summary statistics, but it is trained 10× faster and classifies genomic regions 5× faster by inferring region characteristics from the raw sequence data directly. Deploying ASDEC for genomic scans achieved up to 15.2× higher sensitivity, 19.4× higher success rates, and 4× higher detection accuracy than state-of-the-art methods. We used ASDEC to scan human chromosome 1 of the Yoruba population (1000Genomes project), identifying nine known candidate genes.

A retrospective of deaths related to migration along the southeasternmost land borders of Europe: an update encompassing the years 2015-22.

This study presents an update of forensic accounting of the numbers and demographics of migrants found deceased in the Evros region of Greece in the years from 2015-22. Compared to data from 2000-14, this update reflects the mounting number of border-related deaths in the region, as well as the changing demographic trends associated with the migrants who perish crossing the Greek-Turkish border. Specifically, the paper documents a broadening of locations from which migrants originate, the increasing diversity of migrant death locations, and a shift in the leading causes of death. It contains important forensic accounting of the unique humanitarian crisis occurring along the Greek-Turkish land border while also providing an additional context for the global migration crisis. The data presented here offer insights into other forensic stakeholders impacted by the global migration crisis, with respect to what factors contribute to and detract from identification rates, and can help stakeholders make informed policy decisions.

Association of cytokine gene polymorphisms with peripheral neuropathy susceptibility in people living with HIV in Greece.

Relatively little research has been done in recent years to understand what leads to the unceasingly high rates of HIV sensory neuropathy despite successful antiretroviral treatment. In vivo and in vitro studies demonstrate neuronal damage induced by HIV and increasingly identified ART neurotoxicity involving mitochondrial dysfunction and innate immune system activation in peripheral nerves, ultimately all pathways resulting in enhanced pro-inflammatory cytokine secretion. Furthermore, many infectious/autoimmune/malignant diseases are influenced by the production-profile of pro-inflammatory and anti-inflammatory cytokines, due to inter-individual allelic polymorphism within cytokine gene regulatory regions. Associations of cytokine gene polymorphisms are investigated with the aim of identifying potential genetic markers for susceptibility to HIV peripheral neuropathy including ART-dependent toxic neuropathy. One hundred seventy-one people living with HIV in Northern Greece, divided into two sub-groups according to the presence/absence of peripheral neuropathy, were studied over a 5-year period. Diagnosis was based on the Brief Peripheral Neuropathy Screening. Cytokine genotyping was performed by sequence-specific primer-polymerase chain reaction. Present study findings identify age as an important risk factor (p < 0.01) and support the idea that cytokine gene polymorphisms are at least involved in HIV peripheral-neuropathy pathogenesis. Specifically, carriers of IL1a-889/rs1800587 TT genotype and IL4-1098/rs2243250 GG genotype disclosed greater relative risk for developing HIV peripheral neuropathy (OR: 2.9 and 7.7 respectively), while conversely, carriers of IL2+166/rs2069763 TT genotype yielded lower probability (OR: 3.1), all however, with marginal statistical significance. The latter, if confirmed in a larger Greek population cohort, may offer in the future novel genetic markers to identify susceptibility, while it remains significant that further ethnicity-oriented studies continue to be conducted in a similar pursuit.

Phylogenetic Analysis of SARS-CoV-2 Data Is Difficult.

Numerous studies covering some aspects of SARS-CoV-2 data analyses are being published on a daily basis, including a regularly updated phylogeny on nextstrain.org. Here, we review the difficulties of inferring reliable phylogenies by example of a data snapshot comprising a quality-filtered subset of 8,736 out of all 16,453 virus sequences available on May 5, 2020 from gisaid.org. We find that it is difficult to infer a reliable phylogeny on these data due to the large number of sequences in conjunction with the low number of mutations. We further find that rooting the inferred phylogeny with some degree of confidence either via the bat and pangolin outgroups or by applying novel computational methods on the ingroup phylogeny does not appear to be credible. Finally, an automatic classification of the current sequences into subclasses using the mPTP tool for molecular species delimitation is also, as might be expected, not possible, as the sequences are too closely related. We conclude that, although the application of phylogenetic methods to disentangle the evolution and spread of COVID-19 provides some insight, results of phylogenetic analyses, in particular those conducted under the default settings of current phylogenetic inference tools, as well as downstream analyses on the inferred phylogenies, should be considered and interpreted with extreme caution.

Structural classification of proteins based on the computationally efficient recurrence quantification analysis and horizontal visibility graphs.

MOTIVATION: Protein structural class prediction is one of the most significant problems in bioinformatics, as it has a prominent role in understanding the function and evolution of proteins. Designing a computationally efficient but at the same time accurate prediction method remains a pressing issue, especially for sequences that we cannot obtain a sufficient amount of homologous information from existing protein sequence databases. Several studies demonstrate the potential of utilizing chaos game representation along with time series analysis tools such as recurrence quantification analysis, complex networks, horizontal visibility graphs (HVG) and others. However, the majority of existing works involve a large amount of features and they require an exhaustive, time consuming search of the optimal parameters. To address the aforementioned problems, this work adopts the generalized multidimensional recurrence quantification analysis (GmdRQA) as an efficient tool that enables to process concurrently a multidimensional time series and reduce the number of features. In addition, two data-driven algorithms, namely average mutual information and false nearest neighbors, are utilized to define in a fast yet precise manner the optimal GmdRQA parameters. RESULTS: The classification accuracy is improved by the combination of GmdRQA with the HVG. Experimental evaluation on a real benchmark dataset demonstrates that our methods achieve similar performance with the state-of-the-art but with a smaller computational cost. AVAILABILITY AND IMPLEMENTATION: The code to reproduce all the results is available at https://github.com/aretiz/protein_structure_classification/tree/main. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Significance of regional population HLA immunogenetic datasets in the efficacy of umbilical cord blood banks and marrow donor registries: a study of Cretan HLA genetic diversity.

BACKGROUND AIMS: The high genetic diversity of HLA across populations significantly confines the effectiveness of a donor or umbilical cord blood search for allogeneic hematopoietic stem cell transplantation (HSCT). This study aims to probe the HLA immunogenetic profile of the population of Crete, a Greek region with specific geographic and historical characteristics, and to investigate potential patterns in HLA distribution following comparison with the Deutsche Knochenmarkspenderdatei (DKMS) donor registry. It also aims to highlight the importance of regional public cord blood banks (PCBBs) in fulfilling HSCT needs, especially in countries with significant genetic diversity. METHODS: A cohort of 1835 samples representative of the Cretan population was typed for HLA class I (HLA-A, HLA-B, HLA-C) and class II (HLA-DRB1, HLA-DQB1, HLA-DPB1) loci by high-resolution second field next-generation sequencing. Data were compared with the respective HLA profiles of 12 DKMS populations (n = 20 032). Advanced statistical and bioinformatics methods were employed to assess specific intra- and inter-population genetic indexes associated with the regional and geographic distribution of HLA alleles and haplotypes. RESULTS: A considerable HLA allelic and haplotypic diversity was identified among the Cretan samples and between the latter and the pooled DKMS cohort. Even though the HLA allele and haplotype frequency distribution was similar to regions of close geographic proximity to Crete, a clinal distribution pattern from the northern to southern regions was identified. Significant differences were also observed between Crete and the Greek population of DKMS. CONCLUSIONS: This study provides an in-depth characterization of the HLA immunogenetic profile in Crete and reveals the importance of demographic history in HLA heterogeneity and donor selection. The novel HLA allele and haplotype frequency comparative data between the Cretan and other European populations signify the importance of regional PCBBs in prioritizing HLA diversity to efficiently promote the HSCT program at the national level and beyond.

[Functional and morphological disorders of taste and olfaction in COVID-19 patients]. / Funktionelle und morphologische Geschmacks- und Geruchsstörungen bei COVID-19-Patienten.

OBJECTIVE: This study aimed to test the prevalence and evolution of acute olfactory and gustatory functional impairment and their morphologic correlates in COVID-19 patients who require hospitalization due to COVID-19-related respiratory conditions. METHODS: Included were 53 consecutive hospitalized patients (23 males, 30 females; age 42.54 ± 10.95 years) with an RT-PCR-confirmed COVID-19 diagnosis. Patients were examined twice: just after hospital discharge and 4-6 weeks later. Electrogustometric (EGM) thresholds at the tongue area supplied by the chorda tympani, at the soft palate, and in the region of the vallate papillae were recorded bilaterally. Olfaction was examined by Sniffin' sticks (Burghardt GmbH, Wedel, Germany). The patients' nasal and oral mucosa (fungiform papillae, fpap) were examined by contact endoscopy. Findings were compared to those of 53 healthy individuals matched for sex and age (23 males, 30 females; age 42.90 ± 10.64 years). RESULTS: EGM thresholds in patients were significantly higher than those of healthy subjects at both timepoints. EGM thresholds at the second measurement were significantly lower than those at the first measurement. Accordingly, patient-reported gustatory outcomes were improved at the second measurement. The same pattern was found using Sniffin' sticks. Significant alterations in form and vascularization of fPap were detected in patients, especially at the first instance. Interestingly we did not observe any significant changes in the morphology and vascularization of nasal mucosa. CONCLUSION: COVID-19 affects both gustatory and olfactory functions. In parallel, it also affects the structure and vascularization of both nasal and oral mucosa, albeit the nasal mucosa to a much lesser, non-significant extent. Our findings suggest that COVID-19 may cause a mild to profound neuropathy of multiple cranial nerves.

Evolutionary models of amino acid substitutions based on the tertiary structure of their neighborhoods.

Intra-protein residual vicinities depend on the involved amino acids. Energetically favorable vicinities (or interactions) have been preserved during evolution, while unfavorable vicinities have been eliminated. We describe, statistically, the interactions between amino acids using resolved protein structures. Based on the frequency of amino acid interactions, we have devised an amino acid substitution model that implements the following idea: amino acids that have similar neighbors in the protein tertiary structure can replace each other, while substitution is more difficult between amino acids that prefer different spatial neighbors. Using known tertiary structures for α-helical membrane (HM) proteins, we build evolutionary substitution matrices. We constructed maximum likelihood phylogenies using our amino acid substitution matrices and compared them to widely-used methods. Our results suggest that amino acid substitutions are associated with the spatial neighborhoods of amino acid residuals, providing, therefore, insights into the amino acid substitution process.

Endoscopic sinus surgery outcomes in CRS: quality of life and correlations with NOSE scale in a prospective cohort study.

BACKGROUND: To evaluate the impact of endoscopic sinus surgery (ESS) on clinical outcomes, quality of life (QoL) and Nasal Obstruction and Symptom Evaluation (NOSE) scale in patients with CRSwNP and CRSsNP. An additional question that needs to be investigated is whether there is a correlation between patients at the age of relapse. METHODOLOGY/PRINCIPAL: A prospective cohort study of 150 subjects [96 males, 54 females, mean age: 51.99 ± (15.73)]. The SNOT-22 and NOSE questionnaires were used to measure the patients' QoL and their nasal blockage symptoms, respectively. Endoscopic and computerized tomography (CT) scores depicted the objective findings. RESULTS: Following ESS, the endoscopic scale showed a significant improvement in 83.85% of patients. QoL measured with SNOT-22 improved by 78.85% and with NOSE scale by 92.10%. Also, a statistically significant correlation was found between NOSE, SNOT-22 and the Lund-Kennedy scale. Recurrence was observed in 13 patients during follow-up. There was no statistically significant correlation between age, gender, smoking and recurrence tendency. Patients with baseline SNOT-22 and NOSE scores lower than 30 typically fail to obtain a clinically meaningful benefit. Patients with a rate greater than or equal to 40 achieved a minimal clinically important difference (MCID) of 83.9% and had an average symptom reduction (RI) rate of 60.3%. CONCLUSIONS: ESS is an important treatment option for symptomatic patients with CRSwNP and CRSsNP. Both objective and subjective measurements including QoL improved significantly, and the results stabilized at 12 to 18 months. The NOSE scale is a sensitive outcome measure in the CRS population, including subjects with and without nasal polyps. In our study, SNOT-22 and NOSE are excellent predictors of postoperative improvement.

Electrogustometry: Normative data for stimulus duration, tongue site and age decline.

OBJECTIVES: Our primary goal was to evaluate the effect of stimulus duration on electrogustometry (EGM) thresholds. Additionally, we sought to evaluate any sex-related influences and compare the above results to those of taste strips. DESIGN: Electrogustometry thresholds of various stimulus durations (0.5, 1.0, 1.5 and 2.0 seconds) were measured in 212 non-smokers (age range: 10-80 years, divided into eight age-groups) without self-reported gustatory impairment. Furthermore, taste strips chemogustometry measurements in 132 participants were performed. SETTING: Tertiary referral medical centre. PARTICIPANTS: 212 non-smokers, divided into eight age-groups participated in the study. MAIN OUTCOME MEASURES: Electrogustometry thresholds and taste strips, duration of EGM stimuli. RESULTS: Electrogustometry thresholds increased progressively with age and with stimulus duration from 0.5 to 2 seconds. This pattern was consistent in all six anatomic areas, irrespective of sex. In contrast, when using chemogustometry, no age- or sex-related differences were observed. CONCLUSIONS: Electrogustometry-threshold values increase progressively with age and with stimulus duration. Therefore, we recommend documenting stimulus duration in the future EGM recordings as it may significantly affect EGM amplitude threshold values.

Intraspecific diversification of the crop wild relative Brassica cretica Lam. using demographic model selection.

BACKGROUND: Crop wild relatives (CWRs) contain genetic diversity, representing an invaluable resource for crop improvement. Many of their traits have the potential to help crops to adapt to changing conditions that they experience due to climate change. An impressive global effort for the conservation of various CWR will facilitate their use in crop breeding for food security. The genus Brassica is listed in Annex I of the International Treaty on Plant Genetic Resources for Food and Agriculture. Brassica oleracea (or wild cabbage), a species native to southern and western Europe, has become established as an important human food crop plant because of its large reserves stored over the winter in its leaves. Brassica cretica Lam. (Bc) is a CWR in the brassica group and B. cretica subsp. nivea (Bcn) has been suggested as a separate subspecies. The species Bc has been proposed as a potential gene donor to brassica crops, including broccoli, cabbage, cauliflower, oilseed rape, etc. RESULTS: We sequenced genomes of four Bc individuals, including two Bcn and two Bc. Demographic analysis based on our whole-genome sequence data suggests that populations of Bc are not isolated. Classification of the Bc into distinct subspecies is not supported by the data. Using only the non-coding part of the data (thus, the parts of the genome that has evolved nearly neutrally), we find the gene flow between different Bc population is recent and its genomic diversity is high. CONCLUSIONS: Despite predictions on the disruptive effect of gene flow in adaptation, when selection is not strong enough to prevent the loss of locally adapted alleles, studies show that gene flow can promote adaptation, that local adaptations can be maintained despite high gene flow, and that genetic architecture plays a fundamental role in the origin and maintenance of local adaptation with gene flow. Thus, in the genomic era it is important to link the selected demographic models with the underlying processes of genomic variation because, if this variation is largely selectively neutral, we cannot assume that a diverse population of crop wild relatives will necessarily exhibit the wide-ranging adaptive diversity required for further crop improvement.

Transcriptome reprogramming and myeloid skewing in haematopoietic stem and progenitor cells in systemic lupus erythematosus.

OBJECTIVES: Haematopoietic stem and progenitor cells (HSPCs) are multipotent cells giving rise to both myeloid and lymphoid cell lineages. We reasoned that the aberrancies of immune cells in systemic lupus erythematosus (SLE) could be traced back to HSPCs. METHODS: A global gene expression map of bone marrow (BM)-derived HSPCs was completed by RNA sequencing followed by pathway and enrichment analysis. The cell cycle status and apoptosis status of HSPCs were assessed by flow cytometry, while DNA damage was assessed via immunofluorescence. RESULTS: Transcriptomic analysis of Lin-Sca-1+c-Kit+ haematopoietic progenitors from diseased lupus mice demonstrated a strong myeloid signature with expanded frequencies of common myeloid progenitors (CMPs)-but not of common lymphoid progenitors-reminiscent of a 'trained immunity' signature. CMP profiling revealed an intense transcriptome reprogramming with suppression of granulocytic regulators indicative of a differentiation arrest with downregulation trend of major regulators such as Cebpe, Cebpd and Csf3r, and disturbed myelopoiesis. Despite the differentiation arrest, frequencies of BM neutrophils were markedly increased in diseased mice, suggesting an alternative granulopoiesis pathway. In patients with SLE with severe disease, haematopoietic progenitor cells (CD34+) demonstrated enhanced proliferation, cell differentiation and transcriptional activation of cytokines and chemokines that drive differentiation towards myelopoiesis, thus mirroring the murine data. CONCLUSIONS: Aberrancies of immune cells in SLE can be traced back to the BM HSPCs. Priming of HSPCs and aberrant regulation of myelopoiesis may contribute to inflammation and risk of flare. TRIAL REGISTRATION NUMBER: 4948/19-07-2016.

Bilateral taste disorders in patients with Ramsay Hunt syndrome and Bell palsy.

OBJECTIVE: Ramsay Hunt syndrome (RHS) and Bell palsy (BP) are typically known as facial nerve motor syndromes and are primarily unilateral. The aim of this study was to challenge this assertion, because both conditions are also known to be associated with viruses that typically affect several nerves. METHODS: Ten participants with RHS, 12 with BP, all clinically unilateral, and 12 healthy controls were prospectively enrolled. Electrogustometric thresholds were measured bilaterally in the areas of the chorda tympani, the glossopharyngeal, and the major petrosal nerve. Also bilaterally, the taste function was tested using chemogustometry with different tastant concentrations. Again bilaterally, the morphology of the mucosa and the vessels of the anterior fungiform papillae were examined by contact endoscopy. Statistically, RHS and BP participants were compared with the healthy controls, and the paretic sides of RHS and BP were compared pairwise with their mobile sides. RESULTS: Electrogustometrically, perception was reduced bilaterally in RHS (10-19dB, p < 0.001) and BP (3-5dB, p = 0.011-0.030) in all 3 innervation areas. Chemogustometrically, it was also reduced bilaterally in RHS (20-70%) and BP (8-50%). Papillary atrophies were increased 100% in RHS (p = 0.001) and BP (p < 0.001). They were more increased on the paretic side in RHS (30%, p = 0.078) and BP (83%, p < 0.001). INTERPRETATION: In these 2 clinically unilateral conditions, the gustatory perception and morphology are bilaterally affected, more in RHS and more on the paretic side. BP, known as an isolated motor condition, appears to be a cranial polyneuritis. A bilateral examination and therapeutic gustatory monitoring might follow these observations in evidence-based practice. Ann Neurol 2018;83:807-815.

Comparisons of molecular diversity indices, selective sweeps and population structure of African rice with its wild progenitor and Asian rice.

KEY MESSAGE: The extent of molecular diversity parameters across three rice species was compared using large germplasm collection genotyped with genomewide SNPs and SNPs that fell within selective sweep regions. Previous studies conducted on limited number of accessions have reported very low genetic variation in African rice (Oryza glaberrima Steud.) as compared to its wild progenitor (O. barthii A. Chev.) and to Asian rice (O. sativa L.). Here, we characterized a large collection of African rice and compared its molecular diversity indices and population structure with the two other species using genomewide single nucleotide polymorphisms (SNPs) and SNPs that mapped within selective sweeps. A total of 3245 samples representing African rice (2358), Asian rice (772) and O. barthii (115) were genotyped with 26,073 physically mapped SNPs. Using all SNPs, the level of marker polymorphism, average genetic distance and nucleotide diversity in African rice accounted for 59.1%, 63.2% and 37.1% of that of O. barthii, respectively. SNP polymorphism and overall nucleotide diversity of the African rice accounted for 20.1-32.1 and 16.3-37.3% of that of the Asian rice, respectively. We identified 780 SNPs that fell within 37 candidate selective sweeps in African rice, which were distributed across all 12 rice chromosomes. Nucleotide diversity of the African rice estimated from the 780 SNPs was 8.3 × 10-4, which is not only 20-fold smaller than the value estimated from all genomewide SNPs (π = 1.6 × 10-2), but also accounted for just 4.1%, 0.9% and 2.1% of that of O. barthii, lowland Asian rice and upland Asian rice, respectively. The genotype data generated for a large collection of rice accessions conserved at the AfricaRice genebank will be highly useful for the global rice community and promote germplasm use.

A retrospective statistical review of deaths owing to migration through the southeasternmost land borders of the European Union, Greece 2000-14.

The land borders of Evros, Greece, have been a common entry point for undocumented migrants on their way to Europe through Turkey. Adverse conditions, however, have resulted in many human casualties over the years. On the Greek side, 334 cadavers were retrieved between 2000 and 2014. This study provides a detailed forensic account of the humanitarian disaster in Evros to create an official scientific record of the situation. It showcases the gravity of the global issue of migration relating to health and mortality, and encourages communication and continual improvement of the approach and patterns of practices surrounding the subject. A retrospective statistical research review was conducted of border-related fatalities between 2000 and 2014, assessing the age and gender of victims, the cause of death, the location of bodies, identification rates, and country of origin. Age ranged generally from 24 to 29 years, but infants and children were among the deceased.

Archaic Hominin Introgression in Africa Contributes to Functional Salivary MUC7 Genetic Variation.

One of the most abundant proteins in human saliva, mucin-7, is encoded by the MUC7 gene, which harbors copy number variable subexonic repeats (PTS-repeats) that affect the size and glycosylation potential of this protein. We recently documented the adaptive evolution of MUC7 subexonic copy number variation among primates. Yet, the evolution of MUC7 genetic variation in humans remained unexplored. Here, we found that PTS-repeat copy number variation has evolved recurrently in the human lineage, thereby generating multiple haplotypic backgrounds carrying five or six PTS-repeat copy number alleles. Contrary to previous studies, we found no associations between the copy number of PTS-repeats and protection against asthma. Instead, we revealed a significant association of MUC7 haplotypic variation with the composition of the oral microbiome. Furthermore, based on in-depth simulations, we conclude that a divergent MUC7 haplotype likely originated in an unknown African hominin population and introgressed into ancestors of modern Africans.

Is the Garden Gun (Flobert 9 mm) Capable of Inducing Fatal Injury?: Literature Review and Comparative Presentation of Two Cases.

This article presents both a fatal suicide incident by Flobert 9 mm-type smoothbore weapon with a single-shot projectile and a nonfatal case of a suicide attempt by the same weapon type with a dispersion cartridge from the authors' forensic record. A retrospective study was conducted examining 84 cases involving cases of headshots inflicted by all kinds of weapons deriving from the broader region of Eastern Macedonia and Thrace (Northern Greece) between 2000 and 2015, among which only 1 involved lethal wounding by a Flobert 9 mm (1.19%). Only a single case report of a fatality with such a weapon has been described throughout international literature. A comparative study also follows between the 3 incidents. The authors argue that a prerequisite for the lethal outcome of the shooting is the absolute contact of the weapon to the head as well as its placement at an anatomical point where the bone resistance is relatively lower, so that the intracranial entry of the projectile is possible. It is also more harmful if the cartridge contains a single-shot projectile rather than multiple projectiles of smaller diameter.

VCFtoTree: a user-friendly tool to construct locus-specific alignments and phylogenies from thousands of anthropologically relevant genome sequences.

BACKGROUND: Constructing alignments and phylogenies for a given locus from large genome sequencing studies with relevant outgroups allow novel evolutionary and anthropological insights. However, no user-friendly tool has been developed to integrate thousands of recently available and anthropologically relevant genome sequences to construct complete sequence alignments and phylogenies. RESULTS: Here, we provide VCFtoTree, a user friendly tool with a graphical user interface that directly accesses online databases to download, parse and analyze genome variation data for regions of interest. Our pipeline combines popular sequence datasets and tree building algorithms with custom data parsing to generate accurate alignments and phylogenies using all the individuals from the 1000 Genomes Project, Neanderthal and Denisovan genomes, as well as reference genomes of Chimpanzee and Rhesus Macaque. It can also be applied to other phased human genomes, as well as genomes from other species. The output of our pipeline includes an alignment in FASTA format and a tree file in newick format. CONCLUSION: VCFtoTree fulfills the increasing demand for constructing alignments and phylogenies for a given loci from thousands of available genomes. Our software provides a user friendly interface for a wider audience without prerequisite knowledge in programming. VCFtoTree can be accessed from https://github.com/duoduoo/VCFtoTree_3.0.0 .